The regulator's chief executive, Leslie Titcomb, said on Monday she had learnt of the sale of BHS, then part of Sir Philip's Arcadia retail group, through reading the newspapers.
Arcadia's company secretary has written on behalf of Sir Philip saying she was given advance notice of the sale.
The regulator's spokesman said she had known but with too few details.
The spokesman said: "We did discuss the proposed terms of a potential deal with trustees and the employer, however, we were not given sufficient information at that time to assess the potential impact on the BHS pension scheme."
He added: "As we have launched an anti-avoidance investigation we need to take care not to prejudice our case."
BHS was sold for a Â£1 in March 2015 to a little known group of businessmen called Retail Acquisitions.
It collapsed into administration two weeks ago with debts of Â£1.3bn and two parliamentary committees are investigating it.
The letter to the Work and Pensions Committee and the Business, Innovation and Skills Select Committee said the regulator had been notified by email on 6 February, 2015 that a decision had been taken to market the sale of BHS.
She was also informed that "two parties had already expressed an interest in a solvent transaction and that negotiations were ongoing with both of them", according to the letter.
It goes on to say that later in February 2015, the BHS pension scheme trustees and their advisers were made aware of the terms of the proposed sale and met the proposed purchaser.
The letter also states that Sir Philip understood that the trustees had discussions about the sale with the regulator at the beginning of March.
The regulator then sought an urgent meeting to find out how the proposed sale could affect the BHS pension schemes.
The letter said a meeting between Sir Philip and The Pensions Regulator took place on 4 March, where they were made aware of the "key terms" of the sale.
The regulator's spokesman said: "When addressing the Work and Pensions Select Committee, Lesley Titcomb said that we were not informed of the confirmation of the actual sale of BHS to Retail Acquisitions Ltd until March 11.
"She explained that we were engaged with the trustees and the employer in the weeks leading up to the sale, and that we were aware a sale was a possibility."
During the lengthy parliamentary session, Ms Titcomb said she was unable to answer specific questions about BHS because of her continuing investigation.
Her team is looking into whether BHS' previous owners had avoided their financial obligations to the pensions schemes.
The letter also responded to questions raised by some MPs about the amount of dividend payments paid out by BHS.
The letter said that a total of Â£423m had been awarded  to directors but that there had been no payments made for the past 12 years.
The payments reflected the "significant" profits the business had made for the three years to the end of 2004.
Former Trustees of the BHS pension scheme are due to appear before MPs later this month.
Sir Philip Green, the former BHS boss, says the head of the Pensions Regulator gave MPs "incorrect" evidence.