More than 150 viewers complained after BBC One screened a controversial episode of Spooks on Monday, taking the total number of objections to the episode towards 1,000.
The BBC says producers worked with Muslim leaders to ensure balance
The story centred on a suicide bomb school in a Birmingham mosque and has been condemned for showing Islam in the UK in a bad light.
About 800 people contacted the BBC after the episode was shown on digital channel BBC Three on 2 June urging the corporation not to repeat it on its main channel.
Birmingham Central Mosque was defaced after the BBC Three screening, with the slogan "Suicide bombers inside - kill the bombers".
But the BBC said that the fact that the volume of complaints declined after the BBC One broadcast indicated that viewers realised it was not as bad as they expected.
An average of 7.6 million people saw the show on BBC One, and 150 complaints had been received by 0930 BST on Tuesday.
Muslims groups said the programme's plot could have incited hatred towards Islam.
Inayat Bunglawala of the Muslim Council of Britain said: "We can't deny that the BBC have a right to screen a drama about this - it is topical.
"It is the treatment of the subject that will lead to attacks," he said.
West Midlands Police said there was no evidence that the attack on the Birmingham Central Mosque was linked with the programme.
The BBC defended the show, saying programme-makers liaised with Muslim community leaders in order to ensure balance.
A spokeswoman said: "We do not believe that it incites hatred or disrespect for Muslims or Islam."
"The story is about a Muslim who works to prevent such an attack from happening. The character is inspired by the true story of an Algerian agent, who greatly assisted the British Security Services undercover.
"The drama does not say that mosques breed terrorists."
Spooks, based around a trio of MI5 agents fighting terrorism in the UK, is currently in its second series.