A key figure in a school building programme in England feared his phone was being hacked during an outcry over the government's decision to scrap it.
The government says "a senior education official" complained of "politically motivated" nuisance calls last July.
The BBC understands that the official was Tim Byles, then the chief executive of the body running the Building Schools for the Future (BSF) programme.
The government is not naming the official involved.
It was in July last year that Education Secretary Michael Gove announced he was ending the £55bn BSF programme, leading to the cancellation of 700 projects and to several legal challenges.
He said the scheme was wasteful and inefficient.
Within days, Mr Gove had to apologise to MPs and to local councils over errors which meant some councils were wrongly told their projects were going ahead when in fact they had been cancelled.
Mr Byles was at that time the chief executive of Partnerships for Schools - the body charged by the Labour government with running the BSF programme. He resigned in May.
In July last year there had been a feeling among some at the organisation that the media was being briefed against it, in order to blame it for the errors.
The BBC has approached Mr Byles for comment but has so far not received a response.
Details of the allegations are revealed in letters released by the government.
This was after the matter was raised in the House of Commons on Wednesday in the emergency debate on the phone-hacking crisis, when the prime minister was again criticised for making the former News of the World editor Andy Coulson his head of communications.
Then, the former Labour Minister Nick Raynsford asked: "Will the prime minister confirm that a year ago, during the period when Mr Coulson was director of communications, the cabinet secretary was alerted to evidence of illegal phone hacking, covert surveillance and hostile media briefing directed against a senior official in the government service?"
The prime minister replied that he would look very closely at what Mr Raynsford had said, but added that "in the period that Andy Coulson worked at No 10 Downing Street as head of communications, there was no complaint about the way he did his job".
Now letters dated 21 July, about the allegations, have been released by both the Cabinet Office and the Department for Education.
A letter from the top civil servant at the Department for Education, Sir David Bell, to the Cabinet Secretary Sir Gus O'Donnell says: "In July 2010, a senior official raised concerns with me about media harassment.
"He complained that he was receiving a large number of phone calls from journalists. He also mentioned receiving calls where no-one actually spoke to him."
Sir David says the matter was referred to the department's security officer and that the official involved "suspected his mobile phone had been tampered with, for the purpose of intercepting calls".
The individual then took the matter up with the police and his phone company, Mr Bell said, but neither "was able to identify any malpractice".
At the end of the letter, Mr Bell says he spoke to the individual involved after Mr Raynsford's comments to MPs and that he had "confirmed that at no time did he ever suggest, or even consider, that the telephone calls he received without anyone speaking on the line came from political special advisers at 10 Downing Street.
"The official did though surmise that there was some political motivation behind the calls," the letter ends.
Sir Gus - in a letter to Mr Raynsford - says "at no point did the individual mention covert surveillance to that Department [education] or to me No 10 special advisers in his concern about phone tampering".
Mr Raynsford later rejected suggestions by Sir Gus that the concerns about phone hacking were the result of a "genuine misunderstanding".
He told the BBC he could not reveal who the official was, but that what had happened had been "disgraceful"- and had included people rifling through the official's rubbish.
He said the victim had been subject to "nasty and intensive interest by the media and to hostile media briefings and hacking".
"It's a serious matter which should never happen again," he said.