The Competition Commission is looking into allegations misleading evidence was given to the inquiry into the takeover of the Herald newspaper group.
Newsquest's takeover of the Herald newspapers is to be investigated
Newsquest, which bought the group in 2003, has made £3m of cuts, resulting in 100 job losses at the Herald, Sunday Herald and Evening Times newspapers.
The company told the commission that it would maintain standards when it bought the newspaper group.
The commission is re-examining evidence it received in the original inquiry.
Confirmation of a fresh investigation by the competition watchdog came in a letter to Pete Wishart, the SNP MP for Perth and North Perthshire.
Competition Commission chief executive Martin Stanley told Mr Wishart that his office has seen correspondence which suggested the original inquiry may have heard misleading evidence.
The letter stated: "These are serious allegations and it is clearly for us to examine them."
So far Newsquest, which is owned by the US firm Gannett, has made no comment on the allegations.
Mr Wishart wrote to the commission last month to express his concern about standards and job losses at the newspapers.
The National Union of Journalists (NUJ) has started to ballot members for industrial action after five compulsory redundancies at the Evening Times in Glasgow.
More than 1,600 people have signed a petition from the NUJ to voice their worries about the impact of the Newsquest takeover.
Paul Holleran, Scottish organiser of the NUJ, told BBC Radio Scotland's Newsdrive programme he was "delighted" that Newsquest was being held to account.
He said: "They took over in 2003 and they said that the titles were safe in their hands and they would maintain quality of journalism, that they would invest and they would take the papers forward and that they would protect the diversity of the different papers and their independence, and they've done the opposite.
"They've only owned the titles for four years and in the last three years, there's been redundancies, editorial redundancies.
"I'll give you an example. The Sunday Herald has last week had 200 pages less than it had in 2003 when the company were owned by SMG."