Registration under the 6P program is to be a two step process. First legal foreign workers are registered, then the foreign workers who work in Malaysia outside the sanction of the law.
700,000 foreign workers register under 6P (Malay Mail)
These two articles give some background on why Malaysia is doing what it is doing.
I especially recommend the AP piece at CBS Moneywatch.
Malaysia Launches Amnesty For Illegal Migrant Workers (RTT News)
Malaysia starts amnesty for illegal foreign labor (CBS Moneywatch)
There is, of course, some dissent.
Employers, worker organisations want amnesty programme suspended (The Star)