The move by the securalist Republican People's Party (CHP) added to a growing sense of political tension in Turkey, as Prime Minister Tayyip Erdogan's government approaches 2011 elections.
Earlier this week 71-year-old CHP leader Deniz Baykal quit, saying he was the victim of a government conspiracy to blacken his name. A video purporting to show him in a bedroom with a female colleague had been posted on the Internet.
On Thursday, Erdogan's hopes of holding the referendum in July were dashed, when the electoral commission set the vote for September 12, coincidentally the 30th anniversary of a military coup.
The ruling AK Party, which has roots in political Islam but relies on broader support for its large parliamentary majority, says the reforms to overhaul the judiciary and make the military answerable to civilian courts are needed to deepen democracy and promote Turkey's candidacy for European Union membership.
Critics say the AK Party wants to weaken the judiciary's independence as part of a plan to introduce Islamic rule by stealth, reversing the secular ideals espoused by the founder of modern Turkey, Mustafa Kemal Ataturk.
The AK party, which narrowly escaped dissolution by the Constitutional Court two years ago because of its Islamist ties, denies any such ambitions, and more benign critics liken it to christian democrat parties in Western Europe.
Some analysts say the dispute over reforms could bring forward a general election due by July 2011, when the AK Party will seek a third term in power.
So far, political uncertainty has had little impact on Turkish markets, which are more preoccupied with global sentiment, and are waiting for developments before reacting.
"If the [Constitutional Court] decision comes in favor of the main opposition and the Court halts the referendum process, the political arena is destined to experience hectic days," warned Ozlem Bayraktar at Unicorn Capital.
There was no clear indication when the Constitutional Court might rule. In the past, it has annulled other AK Party reforms and the reform of the court itself is central to the bill.
Some analysts have said that a decision by the court to annul the referendum could precipitate an early election.
But Erdogan said before leaving for a visit to Greece on Friday that a snap vote was out of the question.
Most of the proposed amendments are not contested, as there is broad consensus in Turkey of a need to change a charter drafted after a 1980 military coup.
The controversy is centerd on the reform of the judiciary, a bastion of Turkey's secularist elite.
