The propaganda effort was revealed in a secret Home Office paper seen by The Guardian newspaper.
The Guardian said the unit is deliberately targeting the BBC and other media organisations as part of a global propaganda push.
The operation is being conducted by the research, information and communication unit (RICU), which was established last year by the then home secretary John Reid.
The Guardian quoted directly from the secret paper, entitled 'Challenging violent extremist ideology through communications'.
It said: "We are pushing this material to UK media channels, eg a BBC radio programme exposing tensions between AQ leadership and supporters. And a restricted working group will communicate niche messages through media and non-media."
The campaign is based on a growing belief that al-Qaida is waning worldwide and is vulnerable on issues such as declining popularity, details of atrocities and rejection by credible figures.
The paper also reveals that the propaganda is aimed at "overseas communicators" in embassies and consulates around the world, people that work with influencers and opinion formers.
The disclosure that a Whitehall counter-terrorism unit is promoting content to the BBC and others will raise serious concerns about editorial practice in a highly sensitive area.
It is not the first time that the Home Office's relationship with the media has sparked controversy.
Earlier this month, the Home Office made headlines when it emerged that Ofcom is looking into the making of Home Office-funded ITV documentary 'Beat: Life on the Street' following concerns it broke rules on sponsored programming.
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