Immigration into the UK remains a controversial subject
Immigration Minister Phil Woolas has accused the Office for National Statistics of "playing politics" with population figures.
He said he was "appalled" at the release of figures showing one in nine British residents was born abroad.
In a letter Mr Woolas describes the decision to release the data as "at best naive or, at worst, sinister".
The Tories have accused the government of "bullying" the ONS and trying to "suppress" embarrassing information.
And Lib Dem home affairs spokesman Chris Huhne said the Home Office should get their "tanks off the statisticians' lawn".
The ONS declined to comment on Mr Woolas's intervention.
Downing Street denied the government was trying to intimidate the statistics body, saying the prime minister fully supported its independence.
But the prime minister's official spokesman said the ONS had to be aware of "the sensitivities" surrounding the immigration debate and the government was "questioning" the timing of the release of data which "can have a political bearing".
The ONS figures, published at the same time as figures showing a big fall in the number of East Europeans registering to work in the UK at the end of last year, showed a 290,000 rise in overseas-born UK residents, which reached 6.5 million in the year to June 2008.
They were widely reported in the media and made it on to the front page of two national newspapers.
In a letter released by the Home Office, Mr Woolas said he tried to block the release of the figures, which he claims are "neither new nor informative".
He says they resulted in the government being accused of "whipping up anti-foreign sentiment when it is the independent ONS who are playing politics".
The letter, to Sunder Katwala, general secretary of the centre-left Fabian Society think-tank, has been published in full on the Liberal Conspiracy website.
In it the minister says: "Most people believe that it is the government who have released these figures in this way.
"In fact, it was the ONS with no ministerial involvement and indeed despite my objections.
"What's worse is that the press release which ran to nine pages highlighted the 1 in 9 figure as the main finding.
"So, government gets the blame by some for whipping up anti-foreign sentiment when it is the independent ONS who are playing politics.
"The justification from the ONS who had, out of schedule, highlighted the figure two weeks earlier because it was 'topical' is, at best naive or, at worst, sinister."
He said the figures included 370,000 undergraduates and about a "quarter of a million" people born to armed forces personnel serving overseas, adding: "Surely the distinction between temporary residence and Indefinite Leave to Remain and full citizenship is more useful in framing a mature debate."
Mr Woolas told BBC News he was "appalled" that the ONS had chosen to publish figures on the ground of "topicality".
He accused the ONS of trying to "grab headlines" in order to show it was a "newly liberated and independent body".
He told BBC Radio 4's Today programme: "Releasing figures outside of the schedule because of the topicality may be interpreted as influencing the political debate.
"This is not a black and white area, the idea that there are figures that won't be used and abused by people is naive and I think the ONS should not release figures because they are topical. They should release them on the schedule."
He claimed the figures, which were widely reported in the media, created the impression that one in nine people in the UK were immigrants, which he said was "not the case".
He denied he was trying to intimidate the ONS, claiming "the independence of the ONS is very important" but he said it had to be careful not to "inflame" a sensitive debate.
The government has clashed with the official statistics body, which was granted independence last year in an effort to free it from political influence, on a number of occasions in recent months.
In February, Sir Michael Scholar, head of the newly-created Statistics Authority, which oversees the work of the ONS, took the unusual step of criticising the government's "premature" and "selective" use of knife crime statistics, which it said had been manipulated for political ends.
The government blamed a Downing Street aide for the release of the figures, which it admitted had been too premature.
Also last month, ministers were angered over the ONS's decision to highlight the proportion of foreign migrants getting jobs in the UK.
It was suggested privately that this was an attempt to embarrass Gordon Brown at the height of the Lyndsey oil refinery dispute over his call for "British jobs for British workers."
Shadow immigration spokesman Damian Green, for the Conservatives, has accused the government of seeking to bully the ONS and suppress embarrassing information.
And Mr Huhne, for the Lib Dems, said: "Ministers cannot lay into independent statisticians simply because they do not like the figures they produce or dislike the timing of when they are ready."