The Northern Mindanao region in the south bore the brunt of the disaster, reporting 25 deaths, according to the National Disaster Risk Reduction and Management Council.
While the tunnel discharge was 750 cusecs, the average inflow was 1,687.5 cusecs.
At least two people have died as floods hit five states this week, and authorities have set up hundreds of relief shelters as the number of people displaced grows.
The action was carried out following orders passed by the Ernakulam munsif court on a petition filed by K.P. Saju of Kothad Koduveliparambil, Varappuzha.
The rain may lash the State on Tuesday or Wednesday and continue till November 15, as thundershowers.
The report was prepared without having a proper idea of the topography of Kuttanad or the high probability of flooding in the area, officials said.
The India Meteorological Department (IMD) issued a yellow alert across the state for the next three days.
Karnataka Chief Minister Basavaraj Bommai cited 'unprecedented rainfall and overflowing' water bodies for the deluge.
Several firms, including Wall Street investment bank Goldman Sachs and Indian food delivery company Swiggy asked emplyees to work from home
The body of Shani, 34, who was also washed away along with the girl during the flash flood, was recovered later.