Handling the matter differently would have sparked mass demonstrations and could have destroyed the morale of security police, Van der Merwe testified in Pretoria.
Van der Merwe, head of the security police at the time, said he kept up the charade in the ensuing months and years that the activist had disappeared after escaping from police custody.
Neither former police commissioner Johan Coetzee nor former law and order minister Adriaan Vlok were told that Bopape's body had, in fact, been secretly thrown in the crocodile-infested Komati River.
"In conversations and in letters I wrote, I presented the mock escape as a fact," Van der Merwe said.
He and nine other policemen have applied for amnesty for offences arising from Bopape's death during police torture in Johannesburg on June 12, 1988.
Five of the applicants were directly involved in subjecting Bopape to electrical shocks. They are Lieutenant-Colonel Adriaan van Niekerk, Major Charles Zeelie, Warrant Officer Hendrik Mostert, Sergeant Johan du Preez and Constable Jakobus Engelbrecht.
Brigadier Schalk Visser and Captain Leon van Loggerenberg are seeking amnesty for their role in getting rid of Bopape's body.
Van der Merwe and two other former police generals, Gerrit Erasmus and Petrus du Toit, were involved in covering up Bopape's death.
Van der Merwe testified that Erasmus visited him at his Pretoria home on the afternoon of Sunday June 12, 1988 to inform him of Bopape's death under torture earlier in the day.
Violent attacks in the anti-apartheid struggle were at the time reaching new heights, and members of the security police were literally working day and night to counter this onslaught, Van der Merwe said.
"The security branch was the most important shield... between order and anarchy in the country. In this respect, the morale of security police played a crucial role."
The country was at war and unusual methods were required to fight the enemy.
Van der Merwe said it was also feared that the African National Congress would use Bopape's death to whip up emotions during the commemoration of the June 16, 1976 Soweto riots.
"Erasmus and I, therefore, decided to conceal Bopape's death, and to arrange for his body to be disposed of secretly."
It would have served no purpose to inform his superiors, Van der Merwe said. That would only have compelled them to become involved in a crime.
"I could offer them nothing but a choice between two unenviable possibilities. Whichever course they chose, they would have been in trouble."
Van der Merwe denied his actions amounted to condoning the death of Bopape.
Police realised that assaulting, torturing or killing an individual in detention would cause serious embarrassment for the government and the police.
"There was, nevertheless, sympathy for police members guilty of such actions in efforts to obtain information which could save lives," Van der Merwe said.
Earlier, he testified that the government ordered security police to commit acts outside the law to fight the ANC in the 80s. These included bomb explosions at two Johannesburg buildings used by the ANC.
Van der Merwe said Vlok approved the attack on Cosatu House. Later Vlok told him that former state president PW Botha also wanted Khotso House to be destroyed.
Members of the Vlakplaas police unit carried out both operations.
Security police also staged bogus terrorist attacks. These included actions in townships planned to create the impression that the perpetrators were members of the ANC, Van der Merwe said.
Members were also ordered to create arms caches, which were then "discovered" to provide excuses for cross-border raids on ANC bases.
"On both sides of the battle there were people who inherited the situation. To that extent we were footballs of circumstances, and we did things we would not even have considered otherwise," Van der Merwe said.
The hearing continues.