eliminating records not in (select id ... so SLOW?

I'm doing something like:

delete from table1 where id not in (select id from table2).

both id are indexed.

table1 contains ~1M record table2 contains ~ 600K record and id is
unique.

The box is a 2x dual core Xeon (below 2GHz) with 4Gb ram.
Default debian etch setup.

It has been working for over 2h now.

Is it normal?

--
Ivan Sergio Borgonovo
http://www.webthatworks.it