The article comes as News Corp finalises its submission to the European Commission.
In June, the independent directors of BSkyB rejected an offer from Rupert Murdoch's News Corporation of 700p a share for the 60.9% of the company not already owned by News Corp, because they said it undervalued BSkyB.
The independent directors said they would have recommended an offer worth 800p per share and both parties agreed to restart talks once the regulatory hurdles to the deal were cleared.
It is understood that the merger will be filed for regulatory approval with the European Commission within the next few weeks, possibly within the next 10 days. The final date will depend on what additional evidence is required by the European Commission.
Once the merger is filed, the business secretary Vince Cable has 25 days under European law to decided whether the Government will ask Ofcom and the Competition Commission to examine the case on media plurality issues, the "public interest test".
In an interview on American TV last week, the BBC's Thompson said the merger could lead to an "abuse of power" and have a negative impact on media plurality.
He has also written a letter to Cable, which was also signed by the chiefs of Channel 4, BT, Telegraph Media Group, Daily Mail and General Trust, Trinity Mirror and Guardian Media Group.
In today’s editorial, The Times suggested that Thompson had "embroiled his taxpayer-funded organisation in a political and commercial battle that it should have nothing to do with" and said it expected Vince Cable to make a decision on the merger "guided by the law not pressure group politics".
A spokeswoman for the Department for Business, Innovation and Skills said should Cable decide to intervene, it would be probably be within the UK timeframe of 10 days from the register of a merger.
A spokesperson for News Corporation said: "We have yet to finalise our submission to the European Commission authorities. We trust that, when appropriate, the Secretary of State will make his decision based on merit and bear in mind these complainants are commercial rivals."
A spokeswoman for the EC had yet to respond to requests for comment prior to publication.
Separately, ahead of Sky's annual general meeting next Friday (22 October), shareholders have been advised by independent research and advisory consultancy PIRC to vote against a number of appointments, including the re-election of James Murdoch as chairman.
PIRC recommended investors oppose the re-election of Murdoch because he is a former chief executive and the son of major shareholder Rupert Murdoch, and to also oppose the election of three other non-executive directors, as it believes there is insufficient independent representation on the board.
In addition, PIRC recommends investors oppose Sky's remuneration report because it fails to expand fully on the changes from the last fiscal period.
It cites the example of chief executive Jeremy Darroch’s full-year base salary earnings increasing by 22% from his 2008 earnings, which PIRC believes is not explained completely in the report.