The authorities in West Timor have shot and wounded two Afghan asylum seekers who they say resisted arrest.
The incident comes as the Indonesian police intercept another 40 Sri Lankan asylum seekers in western Java, while 56 remain on board an Australian customs boat the Oceanic Viking off Bintan Island.
Another 250 asylum seekers are still on board a wooden cargo boat at Merak port in western Java's Bantin province.
The ABC reports the 40 most recently intercepted asylum seekers are being held in local accommodation in Labuan-Pandeglang.
Earlier police in West Timor shot and wounded two Afghan asylum seekers for allegedly resisting arrest.
Reports from West Timor say they were shot when a boat carrying 61 Afghan asylum seekers heading for Australia was intercepted by the Indonesian coast guard.
Police said that one of the asylum seekers was shot in the foot and another in the hand after ignoring warning shots and trying to escape.