David Cameron was aware that RAF pilots were taking part in bombing raids over Syria despite MPs having voted against Britain carrying out strikes in the country.
Downing Street said the Prime Minister knew that a small number of aircrew were embedded with US and Canadian forces and "what they were doing".
The news came amid growing pressure for a statement to parliament after the activity emerged in response to a Freedom of Information request.
Currently, Parliament has only authorised UK forces to attack IS targets in neighbouring Iraq, where they are operating at the invitation of the government in Baghdad.
The Prime Minister's spokeswoman told a briefing for journalists: "The PM was aware that UK personnel were involved in US operations and what they were doing".
The PM's spokeswoman said the policy of embedding UK personnel with foreign forces had been in place since the 1950s and was "well known". The Ministry of Defence had been asked about the issue before, she insisted.
She said "upward of a dozen" Britons were embedded with other nations engaged in the counter-IS campaign - although currently none of them are pilots.
Tory backbencher John Baron, who opposed air strikes in Iraq, said that ministers must come to the Commons to explain what had happened.
"We had a major vote. There should be sensitivity on this issue, and we should be very sensitive to the fact that we have military personnel participating, in effect, in military intervention," he told the BBC Radio 4 Today programme.
"Those individuals should be withdrawn from the embedded programme whilst this vote holds sway, while it still has authority, until we vote again.
"This is, at the end of the day, what parliamentary democracy is all about, regardless of the pros and cons of military intervention."
New Liberal Democrat leader Tim Farron said the involvement of RAF pilots in air strikes without the approval of Parliament was "a breach of trust with the British people" that would simply play into the hands of IS - also referred to as Isis or Isil.
"They desperately want the West to attack them and to be seen to attack them. We are utterly playing in to their hands if we do this," Mr Farron told Sky News.
"For us to be involved in this at this stage, without the sanction of the British people through Parliament and without proper thought being given to the way in which we almost strengthen Isis by doing this, seems very wrong."
Labour, which recently indicated it could be prepared to back a fresh vote on extending air strikes into Syria, said that it would be calling on ministers to make a Commons statement on Monday about the role British pilots had played.
"Ministers need to be clear about the extent of their involvement and as clear as possible about any action they were involved in," a spokesman said.
"The programme to embed personnel with allies is extremely valuable to the development of our armed forces but the Government needs to be transparent about the role they play."
Details of the involvement of UK aircrew were disclosed by the MoD in response to a Freedom of Information request from the pressure group Reprieve.
It said that UK military personnel were embedded with units of the US, Canadian and French armed forces taking part in international coalition operations against IS in Iraq and Syria.
"UK embeds operate as if they were the host nation's personnel, under that nation's chain of command," the MoD said in its response.
"These personnel include pilots flying ISR (intelligence, surveillance, reconnaissance) and strike missions against Isil targets using the equipment of those units. Of these three nations, only the USA and Canada are operating in Syrian airspace."
An MoD spokesman said that British personnel were regularly embedded in the forces of other nations, although currently there were no pilots operating in the region. The number who had previously been involved was said to have been in single figures.
"When embedded, UK personnel are effectively operating as foreign troops. That has been the case in Syria, although there are currently no pilots operating in this region," the spokesman said.
RAF planes are already involved in surveillance flights and air-to-air refuelling operations over Syria in support of coalition strike missions.
Following last month's terror attack on British tourists in Tunisia, David Cameron and Mr Fallon indicated they could seek Commons approval for UK warplanes to join the air strikes as well.
However Jennifer Gibson, staff attorney at Reprieve, said the latest disclosures rendered that debate "somewhat obsolete".
"It is alarming that Parliament and the public have been kept in the dark about this for so long," she said.
"Yet more worrying is the fact that the UK seems to have turned over its personnel to the US wholesale, without the slightest idea as to what they are actually doing, and whether it is legal."