The Companies Registration Office (CRO) has issued strike-off warning notices to 12,500 companies that failed to file annual returns for 2001 and previous years.
Companies that are still in default one month after receiving the notice are to be struck off.
The CRO said it expects up to half of the firms selected will file returns and escape being struck off.
The balance will be referred to the Director of Corporate Enforcement for possible follow-up action in regard to the directors.
100,000 companies have been struck off since 1997, with nearly 6,000 of those being removed last year.
Paul Farrell, registrar, says the CRO is looking into ways to monitor the behaviour of company directors more closely. It hopes to see directors of firms that regularly fail to comply facing harsher sanctions than those that have one-off lapses.