The organisation is officially banned from political office in Egypt but many of its members run as independent candidates in elections.
Ninety per cent of the NDP's candidates are standing unopposed, according to party members.
This year's municipal elections will be the first since a constitutional amendment made in 2005, which requires independent presidential candidates to secure the backing of municipal councillors.
Presidential candidates need the support of at least 10 elected members of every local council in at least 14 provinces for their nomination to stand.
About 700 out of 1,700 members of the opposition liberal Wafd party and 400 members of the left-leaning Tagammu party were allowed to register for the elections, according to reports.
Opposition candidates say they have faced bureaucratic hurdles and physical assaults at registration stations.
More than 800 members of the Muslim Brotherhood were arrested in the weeks leading up to the election.
The group said the government was eager to avoid another electoral setback after the Brotherhood gained 20 per cent of seats in parliament, where its members sit as independents because of their outlawed status.
The organisation's candidate list has shrunk to 498 members, from 5,754.
Essam al-Erian, a senior Brotherhood leader, said that more than 3,192 lawsuits have been filed as a result.
It has won 2,664 of these cases, he said.
"The government, however, has refused to honour the court rulings," Erian wrote in an editorial posted on the group's website.
"It has become clear that the National Democratic Party will not face any real competition in the upcoming elections," he said.
International organisations have condemned the government's crackdown against opposition candidates.