The duo, Rajeev Singh and Sanjay Singh alias Guddu Singh were sent to five-day CBI custody starting on Wednesday by a special court. They were arrested by the state police on March 4.
Haque was severely beaten up before being shot dead after he reached Pratapgarh to probe the murder of the village headman, Nanhe Yadav. An angry mob reportedly attacked Haque and his colleagues but the latter allegedly abandoned him. Haq was then killed. Yadav's brother Suresh was also killed.
It was learnt that 300 people were present when the murders took place but many of them disappeared to avoid being asked by the investigators.
Bhaiya has been accused of masterminding the murder of Haque, considered to be an honest and upright police officer. Bhaiya, however, denied any link with the killings and also resigned as the minister.
The CBI, which is yet to question Bhaiya, is likely to face a challenge in convincing the witnesses of the murders to testify. The 10-member probing team has appealed to the villagers to come forward as witnesses and also assured the local people against any sort of harassment. The CBI has also set up a camp office and a helpline number in Pratapgarh.