The decision came on May 16 after heated political discussion over whether the constitutional change was actually required.
A total of 74 out of 101 MPs from across the political spectrum put their signatures to a document calling for the constitutional amendment, which was handed over to the parliament speaker.
"If passed at a referendum, the bill would create a legal basis for Estonia to join the EU," Indrek Meelak, head of the parliament's constitutional committee, said.
"But regarding the accession decision itself, there will be a separate referendum where people can say 'yes' or 'no' to joining the EU," he added.
The two issues will be put to referenda after the March 2003 parliamentary elections, he said.
Under the constitution, Estonians have the last word on state affairs.
The amendment would add a stipulation to the constitution stating that as a member of the European Union, Estonia will need to give precedence to EU law over domestic law.