An Indonesian official said on Sunday that the Indonesian patrol boat tried to drive the Malaysian vessel out of its territorial waters.
"The Malaysian ship violated our waters, because it was travelling 500m off Karang Unarang," said a navy spokesman. "They often provoke us, but we stand by our orders not to react."
Some Jakarta media had described Friday's incidents off East Kalimantan as "collisions" as the Indonesian patrol boat tried to drive the Malaysian vessel out of its territorial waters.
"That's not a collision," the spokesman said. "A brush would be more appropriate. It was caused by the vortex of sea water from the ships, which pull the two together, but that's not a problem, no significant damage was caused."
Some local newspapers reported that the vessels had collided three times on Friday, but no one had been hurt on either side.
Both countries rely heavily on oil and gas for revenues and each has awarded exploration contracts in the disputed area.
Jakarta sent warships and fighter jets to the area last month after the dispute flared again. The two governments quickly agreed to resolve matters peacefully.