The news report, filmed during the Iraq war and which was released into a news pool, has already been shown on ITV News as well as Sky News.
It is understood to have been exposed as fake after a BBC Two film crew, which had filmed a missile being fired from the submarine while at sea, saw the footage.
The bogus report is set to be shown on BBC Two as part of its 'Fighting the War' series on Sunday, alongside the footage shot by the BBC crew, which spent 10 days on the submarine HMS Splendid for real.
It is the second storm the BBC Two documentary has created. In a recent episode, it exposed how a Royal Marine was highly likely to have been killed in a "blue-on-blue" friendly fire incident and not by enemy action as the Ministry of Defence has claimed.
The new allegations will undermine the trust the public has in the integrity of journalists and could threaten the pooling system in which broadcasters share news footage.
As soon as Sky News was alerted to the accusations, it is understood to have suspended two journalists and launched an investigation.
One anomaly in the Sky report shows a close-up shot of a crew member's finger pushing a red button marked "fire". According to the BBC documentary, the missiles are fired by computer rather than by old-fashioned button pushing.
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