About 400 men are refusing to leave the centre after it was closed two weeks ago by Australia, cutting essential services.
Staff from the PNG immigration department raided the centre on Monday, destroying rain water storage and polluting two wells dug this month by refugees.
The refugees said on Wednesday they had cleaned the wells of rubbish, but during last night's daily protest in the centre the men chanted for water.
Refugees in two of the three alternative facilities for the men on Manus have also reported water shortages.
