Tony Blair is facing calls to make a full statement on how much he knew about the US using UK airports to transport terror suspects.
The leaked memo has reignited the row over the flights
Downing Street says all such cases have now been made public after a leaked memo said "there could be more".
The memo advises ministers to avoid detailed questions on "rendition", and stress their anti-terrorist purpose.
Critics claim the US routinely flies suspects to secret detention centres where they could be tortured.
'Move debate on'
The memo at the centre of the row, written on 7 December last year and apparently designed to prepare Mr Blair for that day's prime minister's questions, said officials had discovered two cases from 1998 - one accepted and one denied - of US flight requests.
It says: "We cannot say that we have received no such request for the use of UK territory.
"The papers we have unearthed so far suggest there could be more such cases."
It adds: "It does remain true that we are not aware of the use of UK territory or airspace for the purposes of extraordinary rendition.
"But we think we should now try to move the debate on and focus people instead on (US Secretary of State Condoleezza) Rice's clear assurance that US activities are consistent with their domestic and international obligations and never include the use of torture."
The memo, which was published in the New Statesman, suggests Whitehall officials were worried that US activities may be illegal under international law.
"In the most common use of the term - ie, involving real risk of torture - it could never be legal because this is clearly prohibited by the UN Convention Against Torture," it says.
It also suggests people captured by British forces in Iraq or Afghanistan could have been sent to potentially illegal interrogation centres.
The memo said the government had "no mechanism for establishing" this, adding "though we would not ourselves question such detainees while they were in such facilities".
Ministers have consistently denied any knowledge of illegal detention centres.
New Statesman political editor Martin Bright told BBC Radio 4's Today programme: "What the advice is saying is, 'Look, this is almost certainly illegal. We do not really know whether it has been going on on our territory, but let's try and spin ourselves out of this situation and try and move the debate on'."
Downing Street said the government had been transparent throughout and the leaked memo predated statements by Mr Straw in which he disclosed details of rendition requests.
"This is a classic case of people getting overexcited about getting a leaked memo rather than reading the content of it," the prime minister's official spokesman said.
A Foreign Office spokesman said Mr Straw had already made clear the UK had not agreed, and would not agree, to help transfer people to places where there were "substantial grounds to believe they would face a real risk of torture."
Mr Straw told MPs on 12 December that only two cases, in 1998, had been found where such transfers were approved, and none had been found since 11 September 2001.
On 10 January this year, Mr Straw told MPs a further case, also from 1998, in which the government "declined a US request to refuel a flight carrying two detainees in route to the US", had been discovered by officials.
Downing Street said the examination of the files was now complete and no further cases had been discovered.
But the Conservatives have called on Mr Straw to make a full Commons statement detailing what the government knew.
Shadow foreign secretary William Hague said: "We still need to know from ministers whether they are entirely satisfied that UK airspace and territory has not been used for the transfer of suspects leading to their torture."
Liberal Democrat acting leader Sir Menzies Campbell said he would be writing to Mr Blair to demand a full statement.
"This memo appears to suggest that at least somewhere in the government someone was giving advice to Number 10 Downing Street that rendition was probably illegal, that there was probably an obligation to make investigations," Sir Menzies told BBC Radio 4's Today programme.
It also suggested "apparently unequivocal" statements made by US Secretary of State Condoleeza Rice "may have related to torture but not to cruel and inhuman behaviour", he added.
Sir Menzies said he did not know if there had been a deliberate cover-up, but added "there appears to be grave inconsistencies in the position of the government".