The Anti-Coup Alliance led by Morsi's Muslim Brotherhood movement had initially considered calling on its supporters to vote against the constitution.
"We reject any vote under military rule," said Hamza al-Farawy, a spokesman for the Anti-Coup Alliance, which demands Morsi's reinstatement.
Farawy said the coalition of Islamist groups, which conducts almost daily protests, would launch a boycott campaign.
The referendum on January 14 and 15 is expected to ratify the new constitution, which replaces the one suspended by the military when it ousted Morsi in July.