It sold 22,292 Prius vehicles in June, from 6,231 in the same month a year earlier and from 10,915 in May said the Japan Automobile Dealers Association.
A new model had helped bolster sales, analysts said.
In May the Prius had already become the top-selling car – a category that excludes popular mini-vehicles with engines of up to 660cc.
Honda’s Fit was the second most popular vehicle in the June, with sales of 13,016 vehicles. The firm’s Insight, a hybrid marketed as a cheaper alternative to the Prius, was ranked fourth.
Hybrid cars are powered by both by petrol and electricity.
High oil prices and growing concern about emissions blamed for global warming has encouraged Japanese carmakers to lead the global development of hybrids.
The sale of fuel-efficient vehicles has also been helped by the government making them tax free.
The car industry hopes that hybrid cars will re-energise the flagging market, which has suffered in the global economic downturn.