About 25 human bones were found in Khlong Phadung Krung Kasem, which runs along one side of Government House, by city workers who were cleaning up the canal, reports said.
The clean-up was part of the work to turn the canal into a floating market, a plan initiated by Prime Minister Prayut Chan-o-cha.
The remains were found while members of a police explosives ordnance disposal team, soldiers and workers from the Dusit district office and the Bangkok Metropolitan Administration's drainage and sewerage department, as well as the Ruam Katanyu Foundation were scouring the canal.
They found a white object, believed to be an electrical circuit panel, a tear gas canister which was no longer usable, and more than 25 partial human bones.
The bones were thought to be from the legs, hips and backbones of humans who died at least two years previously. They were handed over to Nang Lerng police to pass them to the Forensic Medicine Institute of the Royal Thai Police Office for examination.
The clean-up was expected to finish today.