The recall is a sign of the technical difficulties dogging the firm's roll-out of the world's first third-generation (3G) network, currently scheduled to begin full operation in October.
DoCoMo - the wireless division of Nippon Telegraph & Telephone - insisted that it was hoping to upgrade the handsets' capabilities, rather than combat a severe technological hitch.
The company has not yet said when new versions of the N2001 may be distributed, but is still hoping to meet the original launch schedule.
The recall of the 1,400 handsets has provoked little surprise in Tokyo, where complaints about the N2001 have been widespread since the first version was released at the end of May.
Users have bemoaned the handset's short battery life, patchy network coverage and its tendency to suffer software crashes.
Sensitive to criticism
DoCoMo is particularly sensitive to perceptions of technical glitches, because concerns over 3G have been a significant factor behind the sharp falls in the market value of telecoms companies since last year.
Big doubts appear to remain as to whether the new services - which demand massive investment by operators - will be sufficiently attractive and competitively priced to prompt a mass upgrading by users from their existing 2 or 2.5G phones.
DoCoMo, which claims about 60% of the Japanese wireless market, has predicted that its 3G service will be nationwide by year-end, and will have attracted 6m users within three years.
The firm has a head start over other potential operators, because its existing i-Mode service, which allows its more than 22m subscribers to receive e-mail and download data via their mobile phone, has proved a hit.