The Congress was leading in Ater in Madhya Pradesh's Bhind district while the BJP was ahead in Bandhavgarh after the first round of counting of votes for the assembly seats.
After the first round, Congress' Hemant Katere was leading in Ater constituency by a margin of 44 votes against BJP's Arvind Singh Bhadoria, an election official said.
BJP's Shivnaryan Singh was ahead in Bandhavgarh against his rival Savitri Singh of Congress with 5,477 votes after the fourth round.
Earlier postal votes were counted.
The bypoll in Bandhavgarh seat was necessitated as MLA Gyan Singh was elected to the Lok Sabha in November last year.
In Ater, the byelection is necessitated following the death of Congress leader Satyadev Katare
The by-elections for the two seats were held on April 9.
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