Germany and France are "preventing Syrians living in their territory from voting", the foreign ministry said.
"France... is carrying out a hostile press campaign" against next month's election, it said in a statement carried by state news agency SANA.
"It has officially informed our embassy in Paris of its opposition to the holding of the vote on French territory, including the Syrian embassy."
French foreign ministry spokesman Romain Nadal implicitly confirmed the decision.
"The organisation of foreign elections on French soil is covered by the Vienna Convention on Consular Relations of April 24, 1963," he told AFP.
"As we are authorised by this convention, French authorities have the right to oppose the holding of this election anywhere on French territory."
He reiterated France's demand for a "political solution" to conflict in Syria as well as a transition process and Assad's departure from office.
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"Bashar al-Assad, who is responsible for the death of 150,000 people, cannot represent the future of the Syrian people," Nadal said.
More than 150,000 people have been killed in Syria's conflict, which began with anti-government protests in mid-March 2011.
Despite the violence, Damascus has set the presidential election for June 3, with expatriate voting to take place on May 28.
Voting in Syria will only be held in government-held territory, and Syrians who fled through unofficial border crossings will be barred from voting abroad.
The foreign ministry said Germany had "joined the countries trying to block the presidential elections in Syria."
It accused Berlin of "supporting, funding and arming terrorist groups in a bid to destroy Syria," referring to the anti-Assad opposition.
"It is not surprising that these countries have taken the decision to prevent Syrian citizens living in their territory from exercising their constitutional right to vote in the embassies of their country," the ministry added.
Syria's opposition and much of the international community have criticised Damascus for its decision to hold the presidential vote, dismissing the ballot as a "farce."