CBI sources said Raja Bhaiya came to the Central Forensic and Scientific Laboratory this morning to undergo the test after a court in Lucknow gave consent for the same.
The MLA had said earlier that he had not changed his statement and was not worried to face any test.
Justifying the test before the court, the CBI had said that Raja Bhaiya was a suspect and the agency should be given permission to conduct polygraphic test on him.
The results of the test, which lasted for nearly 90 minutes, would be made available to the agency in a few days.
Raja Bhaiya, former food and civil supplies minister in UP government, did not evade any questions, sources said.
The results of the test may not be treated as a primary evidence but can always be treated as circumstantial and would give inputs which can be developed after thorough probe.
The agency has filed its charge sheet in connection with the murder, but did not name Raja Bhaiya as accused. The former MLA had been questioned by the CBI on May 15 and 16.
Haq was shot dead on March 2 in Balipur village in Kunda area of Pratapgarh district where he had gone to probe murder of village head Nanhe Yadav.
Haq's wife Parveen Azad had accused Raja Bhaiya of conspiracy after which he had to resign from the Cabinet on March 4.