But Lord Coe said it was common for political figures to become “the pantomime villain” and defended the decision to invite them to present medals.
He said: “There are 500 medal ceremonies, we require over 1,000 people, not just politicians, and from time to time, I know from my own personal experience, you do become the pantomime villain in politics.
“I don’t think that we should read too much into that and I think it’s really important that politicians have been seen supporting the two greatest sporting events in our lifetimes.
“Politicians are bold enough and brave enough to know that sometimes that is the landscape that they are in.”
Ms May was jeered on Tuesday when it was announced she was to present the medals for the men’s 1500m T20, won by Peyman Bazanjan of Iran.
The reception was not quite as hostile as that given to Mr Osborne, who was booed on Monday when the crowd was told he was to present the winners of the men’s T38 400m race with their medals.
But it was more than enough to make Ms May look uncomfortable.
By contrast, Prince Edward, Earl of Wessex, was cheered loudly when he presented winners’ medals, and there was wild applause for British javelin legend Tessa Sanderson as she was introduced.
At Prime Ministers Questions, Labour leader Ed Miliband said the crowd was reflecting the feelings of the whole country.
The Government has been under fire from disabled rights groups for awarding a contract to carry out “fit for work” assessments to Paralympic sponsor Atos.
Rallies have been staged by activists over tests which have been described as “damaging and distressing”.
The Prime Minister also received a less than enthusiastic reception from spectators at the Aquatics Centre on Sunday.
A Downing Street spokesman said the booing would not stop ministers going to the Games. “It is important (they) are seen to be in support of the Paralympics. Ministers have been going and will continue to do so.”
I cant help to think that Ed Miliband was right to ask at Prime Minister Questions time Ed Miliband has said the reshuffle leaves in place the “same old faces and the same old policies” as he clashed with David Cameron in the Commons.
In the first Prime Minister’s Questions since the summer recess, the Labour leader said the government’s economic policy had “spectacularly failed”.
But Mr Cameron said the coalition remained “strong and united”.
The new cabinet has met for the first time while the government has named who will head a review of aviation policy.
At Prime Minister’s Questions, Mr Cameron indicated details of a consultation on airport capacity, including the controversial issue of a third runway at Heathrow, would be announced shortly.
Hours later, it was announced that Sir Howard Davies – a former chairman of the Financial Services Authority and director-general of employers group the CBI – would chair an independent commission to look at all options for airport capacity in the UK.
Mr Cameron told MPs he would not break his party’s 2010 election promise barring expansion at Heathrow during the course of this parliament.
London’s Conservative Mayor, Boris Johnson, has urged Mr Cameron to go further and reject the idea out of hand while business leaders and some Tory MPs are demanding the project should be back on the agenda to help bring the UK out of recession.
The first parliamentary confrontation between Mr Cameron and Mr Miliband since MPs returned to Westminster from their summer break was dominated by Tuesday’s reshuffle and the state of the economy.
Mr Miliband criticised the promotion of Jeremy Hunt to Health Secretary and, referring to Ken Clarke’s new job as minister without portfolio and George Osborne remaining at the Treasury, he said the government would now have “two part-time chancellors”.
“It is the same old faces, the same old policies, a no-change reshuffle.”
This is a government that means business. We have got the team to deliver it”
Attacking government policies to try and get the country out of recession, the Labour leader said initiatives to build new roads and houses and boost investment in infrastructure had failed to happen.
“His fundamental economic approach is wrong. In his two-and-half-years as prime minister, the British economy has not grown at all. Why does he not admit it the real problem is that ‘Plan A’ has spectacularly failed.”
In a reference to senior cabinet ministers – including Mr Osborne – being booed recently at the Paralympic Games, Mr Miliband claimed the “crowd had spoken for Britain”.
But Mr Cameron said the reshuffle was based on getting every government department to focus on boosting growth, not just the Treasury and the Department for Business, Innovation and Skills.
“This is a government that means business. We have got the team to deliver it.”
Mr Cameron said 900,000 jobs had been created in the private sector since the 2010 election and investment in infrastructure was increasing.
And he contrasted the “strong and united” coalition between the Tories and Lib Dems with what he said were divisions in Labour ranks and Mr Miliband’s inability to assert his leadership over economy policy.
“The big difference in British politics is that I don’t want to move my chancellor, he can’t move his shadow chancellor,” he said. “In spite of all the opportunity, this is a weak and divided opposition.”
David Cameron later chaired the first meeting of the new cabinet, the 80-minute gathering in Downing Street focusing on the economy and future announcements on growth.
Mr Cameron has also been finalising the appointment of junior government ministers.
Tourism Minister John Penrose confirmed he would be leaving the government as the number of posts in the Department of Culture, Olympics Media and Sport is being reduced.
Downing Street earlier said it was setting up a new cabinet committee to oversee the implementation of growth measures, chaired by Mr Osborne.
The move – which follows the appointment of a number of new middle-ranking ministers to the Treasury and Business departments – was applauded by small business.
“It is a welcome step to help drive forward measures to cut red tape, streamline planning rules and get big infrastructure projects moving,” said Federation of Small Business chairman John Walker.
“However, it must be joined up with other areas of government and actually bring about action rather than just rhetoric.”
Meanwhile, Downing Street has recommended to the Queen that several MPs who lost their jobs in the reshuffle receive honours.
Among these, it says former House of Commons leader Sir George Young should be appointed to the Order of the Companions of Honour.
And it recommends knighthoods for former agriculture minister James Paice, former solicitor general Edward Garnier and former defence ministers Nick Harvey and Gerald Howarth.
Downing Street has confirmed more changes to junior ministerial posts:
Don Foster as Parliamentary Under Secretary of State at Dept for Communities and Local Government
Mark Simmonds as Parliamentary Under Secretary of State at Foreign and Commonwealth Office
Lynne Featherstone as Parliamentary Under Secretary of State at Dept for International Development
Brandon Lewis as Parliamentary Under Secretary of State at Dept for Communities and Local Government
Jo Swinson as Parliamentary Under Secretary of State at Dept of Business Innovation and Skills
Lord Marland as Parliamentary Under Secretary of State at Dept of Business Innovation and Skills
Andrew Murrison as Parliamentary Under Secretary at the Ministry of Defence
Edward Timpson as Parliamentary Under Secretary at Dept of Education
Stephen Crabb as Lords Commissioner HM Treasury and Parliamentary Under Secretary of State in Wales Office
Nick Boles as Parliamentary Under Secretary at Dept for Communities and Local Government