"We cannot accept the participation of the parties who committed crimes against the Syrian people in the transitional governing body," HNC spokesman Salem al-Meslet said on the sidelines of peace talks in Geneva.
But he added that the opposition could cooperate with regime "diplomats and technocrats", provided they had support among the population.
He said it was "premature" to discuss specific individuals who could be included in a prospective new government.
"The distribution of seats of the transitional governing body will be subject to a long debate," al-Meslet told AFP.
The government delegation, which arrived in Geneva today, held its first meeting with United Nations mediator Staffan de Mistura, with a second session set for Monday.
The HNC was holding its second meeting with de Mistura today evening.
Political transition in the war-ravaged country, and particularly Assad's future, are the key obstacles at the negotiations, which aim to set up an interim government in six months ahead of UN-monitored presidential and parliamentary elections within 18 months.
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