His warning comes days after international judges issued an arrest warrant for him on charges of war crimes in Darfur.
'We expelled the organisations because they threatened the security of Sudan,' he told a rally in the capital of north Darfur El Fasher.
'We will expel anyone who goes against Sudanese law, whether they are voluntary organisations, diplomatic missions or security forces.'
Sudan has already closed 13 foreign and three local aid groups saying they helped the International Criminal Court (ICC), which last week issued an arrest warrant for Mr al-Bashir over charges he masterminded atrocities in Darfur.
The UN says the expulsions will leave 1.1m people without food, 1.5m without health care and more than 1m without drinking water.
