Tuesday's ruling followed complaints by political groups, secular politicians and constitutional experts over the parliament's decision to give lawmakers half the seats on the 100-member panel.
Islamist groups have insisted that lawmakers get half the panel's seats, prompting charges that they wanted to monopolise the process and give the new constitution an Islamist slant.
About two dozen members, many of them members of liberal groups that engineered the popular uprising, have quit the panel, protesting the selection process and alleging that it was not inclusive enough.
Critics have maintained that the way the panel was picked violated a constitutional declaration adopted in a referendum last year.
The injunction slapped on the decision by parliament could delay the introduction of a constitution needed urgently to clarify the powers of Egypt's new head of state, due to take over from ruling generals by mid-year.
Egypt’s diversity
Ali Fekri, the judge, said the court "rejected the argument that the court is not specialised and decided to halt the decision" that formed the assembly.
He passed on the case's documents to a judicial panel for a review.
This case is one of several lawsuits that had demanded the dissolution of the assembly because it did not represent the diversity of Egyptian society.
The ruling is a blow to the Islamists, who won the majority of seats in Egypt's first free parliamentary vote in decades, following the ouster of President Hosni Mubarak in February last year.
Last week, the Muslim Brotherhood reversed an earlier decision not to field a candidate in presidential elections due on to begin on May 23.
In a surprise move, the group put forward businessman Khairat el-Shater, the Brotherhood's deputy leader, as their choice for the presidency.
The Brotherhood's actions have led many to believe that the group, emerging from some 60 years on the sidelines as an outlawed organisation under Mubarak, was more interested in dominating the country than in an inclusive transition that lays the foundation for a democratic and free Egypt.