Mohaqiq is the head and founder of the Wahdat-e-Mardum Afghanistan political party. He is currently a
member of the Afghan parliament (Wolesi Jirga). Mohaqiq was also a vital member of the Islamic Unity Party (Hezb-e Wahdat-e Islami),
headed by Abdul Karim Khalili. He also served as Planning Minister in the transitional government until he was allegedly fired in March 2004. Mohaqiq claims he was fired after announcing that he would be running in the 2004
presidential elections against Hamid Karzai, however, Karzai's spokesman denied he was fired and claimed Mohaqiq quit after a dispute with the Finance Minister (Ashraf Ghani). Mohaqiq stated that Karzai's
administration was ethnically biased, and that there are attempts to sideline former Mujahideen members from the government.
In the 2004 Afghan presidential elections, Mohaqiq placed third behind Hamid
Karzai and Yunus Qanuni.