The judge adjourned the trial, which opened on Monday, to give more time to protect witnesses.
One woman and 31 men are on trial, including a cleric from the Tabliq sect.
The prosecution did not give any further details about the alleged attack on the witness but did say a court case had started on Friday.
The spate of killings included the head of Uganda's Shia community, Sheikh Abdu Kadir Muwaya, who was shot dead Christmas Day 2014 in Uganda's capital Kampala.
Three days later Sheikh Mustafa Bahiga, a leader of the Tabliq sect was also shot dead.
Sheikh Muhammad Younus Kamoga was one of the Tabliq sect's leaders in Uganda at the time of his arrest.
The BBC's Patience Atuhaire reports from the High Court that the defence said police took the suspects out of jail and forced them to give information against each other.
Our correspondent adds that Judge Ezekiel Muhanguzi ruled that no suspects should be taken out of jail anymore and if police and other agents want access to them, it should be in the presence of their lawyers.
The case is set to resume on 18 July.(BBC)