More than 9,230 hectares (22,800 acres) of agricultural land is underwater in the Shkodra region, including villages where the only means of transport is by boat, the defence ministry said.
Army personnel are evacuating residents and securing food supplies in the affected areas, 100 kilometres (60 miles) north of the capital, Tirana.
The torrential rain in recent days has caused landslides damaging dozens of homes and flooding roads, said the transport ministry.
The rain has also forced the Albanian authorities to release excess water from a hydroelectric plant, which has added to the flooding in northern areas of the country.
Weather forecasters say the rain is likely to ease from Saturday.
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