The comment comes in the backdrop of India's protest on China's move to put on hold New Delhi's attempt to list Jaish-e-Mohammed (JeM) leader Masood Azhar on the UN terror list.
The US, Britain and France had strongly supported the move.
Parrikar said he raised the issue during his visit to China. "I said there can't be differentiation (vis-a-vis) terrorists. All terrorists are the same and they need to be dealt with in the same manner."
The minister spoke to reporters on the sidelines of the Naval Commanders Conference here.
External Affairs Minister Sushma Swaraj had also raised the issue with her Chinese counterpart Wang Yi in Moscow this week.
Talking about his visit to China, Parrikar said the talks were held in a "frank and positive" atmosphere and both sides agreed to step up interactions.
He said "better communication" was the need of the hour. "We agreed to increase our interactions and better management of borders."
He said the "best solution" for border disputes was to finalise the Line of Actual Control (LAC) as different perception of the border leads to what is perceived as transgression.
"Because of different perception, technical transgression happens. We feel it is traversing, but they (Chinese troops) are just patrolling. They come and go," he said.
The minister stressed that such incidents had come down.