The boat, carrying vital supplies of drinking water, rice, and purification tablets, hit a submerged tree trunk as it travelled by river through the disaster zone.
Much of the aid was lost, but no one was injured.
"Apart from the delay in getting aid to people we may now have to re-evaluate how we transport that aid," said Michael Annear, disaster manager in Yangon for the International Federation of Red Cross and Red Crescent Societies.
Supplies have slowly begun to make their way into isolated Myanmar, but relief workers are frustrated over restrictions by the ruling junta, which has refused to allow foreign experts in to direct the recovery effort.
"Some opening-up on the part of the authorities is allowing us to get these materials to their destination," said Stephan Goetghebuer, director of operations of medical charity Medecins Sans Frontieres (MSF).
"But it's no more than a drip-feed, really, given a serious response is more than required.
We still need more back-up aid and