National Epidemiology Centre chief Eric Tayag said patients were suffering severe stomach pains and diarrhoea but added that field doctors were trying to verify if all the cases were due to cholera.
Tayag said the patients "were showing cholera symptoms" and most came from the settlement of Tagoloan in southern Misamis Oriental, where heavy rain has caused minor flooding which could have contaminated the drinking water supply.
The Red Cross said water samples taken from the area were being tested.
A Red Cross official in Manila told AFP the charity's chapter in Misamis Oriental had confirmed that two people had died and that nine out of the 10 villages in Tagaloan were reporting suspected cholera cases.
"We are continuously monitoring the situation and are expecting more field reports to come in later in the day," said the official, who did not want to be named.