The chunky computer-like handset -- with slide-out keyboard and a touch screen -- has found support among hard-core technology specialists but failed to attract a wider audience.
A spokesman for Nokia, the world's top cellphone maker, declined to comment on the sales number, saying the company was pleased with sales, but an executive was more bullish.
Sales have substantially exceeded expectations, Alberto Torres, head of Nokia's solutions business, told the Open Mobile Summit trade conference in London this week.
Nokia has been unable to mount a serious challenge to Apple three years after the iPhone's launch. Its last hit smartphone model, the N95, was unveiled in 2006.
The sales of less than 100,000 N900s compares with sales of 8.75 million iPhones in January-March alone.
The N900, which went on sale last November, is Nokia's first phone running the Linux Maemo operating system, which analysts see as a key for Nokia to regain ground in the coming years.
In February this year Nokia unveiled a plan to merge Maemo with Intel's Moblin operating system.
Nokia sold 50,000 N900s in the last quarter of 2009, and quarterly sales fell in January-March, Gartner statistics showed. Gartner does not track phone sales per model, but as the N900 is the only phone using Maemo, the statistics for operating systems show sales for the model.
(Editing by David Cowell)