''Human waste could be present in small amounts but it's highly unlikely to be responsible for the color of the water,'' he said.
Earth-laden run-off or algae was a more likely cause for the discoloration, he said.
Results of tests on water quality samples taken at Patong beach on Friday won't be known for a few more days, he said.
''We only have a small staff and the survey crew is now in Krabi,'' he said.
Water quality checks are to be made regularly at 23 beaches points around Phuket so tourists will be able to know they are swimming in ''safe'' water.
Friday's sample was the first to be taken right on a Phuket beach, where tourists swim. Previous tests have been taken 100 metres and 500 metres out to sea, according to international standards.
The move to beach testing comes with the support of Phuket's honorary consuls and Phuket Governor Maitree Intrusud, who was at Patong beach on Friday to see the first samples taken.
The color of the water at Patong has generated concern but Dr Somkiat said that natural causes were likely to have triggered the change.
'Human waste would be total coliform and that would turn the seawater black,'' he said. Results are likely to be known in a few days.
''So far Phuket's seawater is fine at the beaches but if Phuket wan'ts to encourage more tourists, then frequent tests should be made,'' he said.
The marine biological centre was short-staffed and more funding would help to improve testing - which now takes place every two months - protect Thailand's tourism future, Dr Somkiat added.
Most onlookers are waiting to see whether test results that show high bacterial levels bring prosecutions against polluters.
Seawater quality is likely to be among the topics for a Coastal Water Safety Summit being planned for Phuket in October, with the support of the British Embassy.