Gen Ilker Basbug said this was in protest at a bill passed by the French National Assembly to make it a crime to deny the Armenian "genocide".
Armenia says Ottoman Turks killed 1.5 million people systematically in 1915 - a claim strongly denied by Turkey.
Both France and Turkey are members of the Nato military alliance, and Turkey is a market for French-made weapons.
So Gen Basbug's announcement that his country is suspending all military ties with France shows the strength of Turkish feeling, says the BBC's Ian MacWilliam.
"Relations with France in the military field have been suspended," said the general, who is head of Turkey's land forces and number two in the armed forces hierarchy.
"High-level visits between the two countries are not being made," he added.
He did not specify whether French firms would be excluded from tenders for military contracts.
French-Turkish trade amounted to 8.2bn euros (£5.5bn; $10.5bn) in 2005, the French news agency AFP reports.
The dispute comes amid worsening relations between Turkey and the European Union - of which France is also a key member.
Some European leaders say Turkey is not making sufficient progress in membership talks to join the union.
The new French bill, tabled by the opposition but opposed by the French government, needs approval from the Senate and president before it becomes law.
It is unlikely to become law because President Jacques Chirac opposes it, our correspondent adds.
The bill provides for a year in jail and a 45,000-euro (£30,000) fine - the same punishment that is imposed for denying the Nazi Holocaust.
Many people in Turkey see it as yet more criticism from Europe as Turkey's EU membership talks stumble on.
The EU and Turkey are already at loggerheads over Cyprus.
Turkey has refused to extend its customs union to include Cyprus, an EU member, until an international embargo of Turkish-controlled northern Cyprus is lifted.
