Police are reporting Channel 4 to the media regulator Ofcom over the way an undercover programme was edited.
But charges will not be brought against preachers featured in Dispatches, which tackled claims of Islamic extremism.
West Midlands Police carried out its own inquiry into three speakers in the Undercover Mosque broadcast, and then into the programme-makers themselves.
The Crown Prosecution Service said the show "completely distorted" what the trio said, a claim Channel 4 rejects.
Kevin Sutcliffe, commissioning editor for Dispatches, said West Midlands police had produced no evidence to support their claims.
"We find it extraordinary that they have gone public on these concerns without discussing them with us first," he said
We believe the comments made in the film speak for themselves - several speakers were clearly shown making abhorrent and extreme comments."
He said the one-hour documentary, which was made over a nine-month period and broadcast in January, allowed comment to be seen in a fuller context.
"All the speakers featured in the film were offered a right to reply and none denied making these comments, nor have any of them complained to Ofcom to our knowledge."
Bombings 'justified'
The Metropolitan Police said on Wednesday that a second Dispatches programme was also being investigated.
Britain Under Attack featured a man known as "Abu Mohammed".
He disguised his face with a scarf in the programme, which was shown on Monday, and said British Muslims were in "a state of war" and the 7 July bombings were "justified".
A Met spokesman said: "We are assessing the content of a Dispatches programme broadcast on Monday 6 August to determine if any offences may have been disclosed."
The spokesman said it was too early to say whether officers were investigating the people shown in the broadcast or the programme-makers.
The January programme infiltrated a number of mosques, one of which was Green Lane Mosque in Small Heath, Birmingham.
'Moderate tradition'
It investigated mosques run by organisations claiming to be dedicated to moderation.
Abu Usamah, one of the preachers from Green Lane Mosque featured in the programme, said he was shocked when he saw himself depicted.
"It was the fact that Green Lane Mosque has a 33-year-old tradition of preaching and teaching the moderate version of Islam.
"To try and demonise the efforts of these people by taking their comments out of context was shocking."
Mr Usamah said he had been featured as saying homosexuals should be thrown from a mountain when in fact he was explaining it was an opinion featured in some books, which was not one he believed.
An undercover reporter claimed to provide evidence that certain speakers preached messages of religious bigotry and extremism.
In a piece about the programme, the Channel 4 Dispatches website said a reporter had attended talks at mosques and found preachers "condemning the idea of integration into British society, condemning British democracy as un-Islamic and praising the Taliban for killing British soldiers".
Police said they acknowledged some parts of the programme may have been considered offensive, but, when analysed in full context, there was not enough evidence to bring charges.
'Completely distorted'
The police investigation was extended to include looking at issues relating to the editing of the programme.
Crown Prosecution Service (CPS) lawyer Bethan David scrutinised 56 hours of media footage, only some of which was used in the broadcast.
She said: "The splicing together of extracts from longer speeches appears to have completely distorted what the speakers were saying.
"The CPS has demonstrated it will not hesitate to prosecute those responsible for criminal incitement.
"But in this case we have been dealing with a heavily-edited television programme, apparently taking out of context aspects of speeches which in their totality could never provide a realistic prospect of any convictions."
Police asked the CPS to consider a prosecution of Channel 4 under the Public Order Act 1986 for showing material likely to stir up racial hatred, but they were advised there was insufficient evidence.