The move came after a meeting between Finance Minister Saleem Mandviwalla and HEC chairman Javed Leghari.
The government had pledged Rs15.8 billion to the HEC in the 2012-13 budget for development grants, which are used to provide for scholarships, infrastructure development and other development projects at public sector universities as well as the salaries of project staff.
But the government has just provided Rs7.9 billion. The last it paid was Rs4.73 billion in December.
The HEC is also awaiting recurring funds to the tune of another Rs3 billion for the third quarter, The Express Tribune quoted Leghari as saying.