Vlok is applying for amnesty for bomb attacks on Cosatu House, Khotso House and cinemas where the film Cry Freedom was being screened.
Cosatu House and Khotso House were the Johannesburg headquarters of the Congress of SA Trade Unions and the SA Council of Churches respectively.
Vlok said he did not report the bombing of Cosatu House to the State Security Council, set up in 1985 to control the deteriorating unrest situation in the country, and the council also did not ask him about the bombing.
"Are you telling us that a bomb blast in the middle of the biggest city in the country was never discussed at the State Security Council?" committee chairman Judge Andrew Wilson asked Vlok.
Vlok replied that it was never discussed.
Vlok also denied the police attack on Cosatu House in 1987 was part of a countrywide government campaign against the trade union. Vlok said the government considered Cosatu an important element in calming the explosive situation that prevailed in the country at the time.
"We knew it was a strong labour movement and were careful not to act against the leadership. However, it's a pity Cosatu did not concern itself with only labour matters and became involved in other activities," Vlok said.
He said it was decided to take action against the union's headquarters to prevent it being used to plan and carry out revolutionary activities. He said after Cosatu House was bombed many of these activities stopped.
He denied there ever was a plan to launch a countrywide campaign against the trade union federation.
When Vlok was asked about a series of attacks on Cosatu offices and officials around the country at the time, he said he knew nothing about them. He said he was sorry he allowed a situation to arise in which incidents such as these occurred. However, there were so many incidents of violence occurring around the country at the time that it was difficult to control the situation.
"But it not possible for me to take resonsibility for everything that happened," he said.
Vlok was also closely questioned about his decision to bomb Khotso House.
Answering a question from Eric Dane, appearing on behalf of the SACC, Vlok said police never had any evidence that the SACC had ever acted unlawfully.
He agreed that the churches represented by the SACC had also not committed any unlawful acts, but said police at the time believed there were individuals in the various churches who were abusing facilities at Khotso House.
Asked why it had been necessary to attack the SACC, Vlok replied that it was the building that was the target and not the religious institution itself.
Comittee chairman Judge Andrew Wilson then said: "If someone blows up my house I would consider that an attack on me."
Vlok insisted that the attack was against individuals who had links with the ANC's armed wing Umkhonto we Sizwe who were making use of Khotso House.
Earlier on Monday, former security police captain Michael Bellinghan said the government's propaganda campaign against anti-apartheid activists was implemented by all government departments.
He said Stratcom, (stratetic communications) was set up to manipulate propaganda and had representatives in all government departments, including Education and Training and Foreign Affairs.
He said it was decided to act against the SACC because its support for the anti-apartheid movements in the 1980s tipped the scales against the government in the propaganda war.
He said up to then the government had claimed it was fighting for Christian values, but the SACC's decision to align itself with the people fighting against apartheid changed the balance. This led to more international pressure on the government which was becoming increasingly isolated.