Power producer Ken Gen has started discharging water from Masinga Dam into River Tana after the reservoir filled up.
Water in the dam has risen to 1,056.68 metres against a maximum level of 1,056.50 metres.
KenGen is discharging 70 cubic metres per second.
On Tuesday, the Energy Cabinet Secretary Charles Keter asked residents of Garissa, Hola, Garsen and Bura to move to safer ground and announcing the dam would start overflowing after it fills to capacity.
"Masinga is the biggest dam. Already there has been spilling in the other dams such as Kiambere. From anytime between now and Friday the way the weather is we will be expecting Masinga to spill. This is an alert we are raising," Mr Keter said.
Masinga Dam feeds four other dams downstream, which are already full.
According to Mr Keter, once Kiambere dam overflows, the estimation is that it will take four days for the cascading water to reach Garissa Town and then lower Tana Delta.
Two weeks ago, homes and farms were submerged by water rendering Garissa and Tana River families homeless.