(AFP) The government will hold an inquiry into the fatal shooting of a local fisherman by an Indonesian navy patrol boat, Defence Minister Najib Razak said today.

"We want to know what actually happened. We are viewing this matter very seriously in that it involved the life of a Malaysian fisherman and the livelihood of his family," he told reporters.

The Indonesian navy says it was forced to open fire on Monday after a trawler skippered by Heng Beng Hong, 43, tried to ram its patrol boat in Indonesian waters.

But the dead man's colleagues said they were all in Malaysian waters, about nine kilometres from the sea border in the Malacca Strait, when Heng was shot.

They said the Indonesian boat sped towards them and started firing without warning.

Some 1,000 Malaysian fishermen from Perak stayed home yesterday saying they are too scared to go to sea following the shooting.

They said Indonesia naval craft had ventured into Malaysian waters since last week.

Najib said the inquiry would establish whether the shooting happened in Indonesian waters. He said it was only justifiable to open fire in self-defence in a threatening situation.

If the inquiry found in favour of the dead man, the cabinet would decide on a suitable response to Indonesia.

The defence minister assured fishermen that the Malaysian navy and police would step up patrols.