The referendum scheduled for Wednesday asks Egyptians to vote on changes to the constitution to allow multi-party candidates.
It has been criticised by opposition members, who label it as little more than window-dressing on the part of the government to appease reformists.
Most of the main opposition parties have declared a boycott of the referendum, and are encouraging Egyptians to stay at home that day rather than vote.
In his lawsuit on Monday, veteran Marxist opposition leader Rifaat Said from the Tagammu party argued that the referendum should be on each item in the article, rather than on the whole, but his lawsuit was dismissed by the court.
Judge Faruq Abd al-Qadir on Monday said the voting system did not violate the law.
Egyptian opposition parties have
given a referendum boycott call
Another lawsuit filed by a group of independent lawyers to have the referendum cancelled, was also thrown out with the judge saying the "case was not within its jurisdiction".
A third lawsuit objected to the interior minister's decision to allow people who were not members of the judicial system to lead some of the referendum supervising committees.
The court said the minister was not breaching the law by doing so, and dismissed the suit.
The court's verdicts could be appealed through the Supreme Administrative Court.
In power since 1981, President Hosni Mubarak has been regularly reinstalled in yes/no referendums in which his name is the only one on the ballot. He has not formally said he will run again, but is widely expected to do so.
Opposition groups claim the proposed changes to the constitution make it harder for those candidates who do not belong to Mubarak's National Democratic Party to run for office.
Amin Iskandar, an activist of the Egyptian Movement for Change (Kifaya), said the opposition would stick to its decision to boycott the referendum.
"We, all political groups and popular movements, will boycott the referendum if legal measures are not taken to cancel it," he told Aljazeera.
Asked whether voting "no" was an option instead of boycotting the referendum, Iskandar said it was not given that there was no certainty that the "no" votes would be properly tallied.
He said Kifaya's boycott campaign would start with political disobedience and end with civil disobedience.