"Delhi Metro is directed to put on hold any further hike till Delhi government completes its enquiry and forms an opinion on this subject," Delhi Transport Minister Kailash Gahlot said.
Delhi Metro fares are set to increase by a minimum of Rs 10 from next month.
"The proposed fare hike by Delhi Metro is likely to adversely affect the interests of a large number of commuters in Delhi," the Aam Aadmi Party leader said. "Delhi Government is completely against any hike in Metro fares."
The minister said it was not clear whether the Delhi government's stand was considered by the fare fixation committee of Delhi Metro.
He said a meeting took place between the Delhi government and DMRC Managing Director Mangu Singh.
The minister's directive came after Delhi Chief Minister Arvind Kejriwal asked Mr Gahlot to find a way to stop the "anti-people" Metro fare hike within a week.
The minister then sought "all relevant records of (the) uncalled fare hike".
Delhi Metro fares are set to increase for a second time this year from October 1.
The last increase was in May when the minimum fare went up from Rs 8 to Rs 10 and the maximum from Rs 30 to Rs 50.
Delhi Metro fares rose following the recommendations of the fourth Fare Fixation Committee.
DMRC was formed in 1995 with equal equity participation of the central government and the government of the National Capital Territory of Delhi. After beginning its operations in 2002, Delhi Metro now covers 218 km with 164 stations. The network is set to expand further.