The Brotherhood condemned the sweeps as a "pre-emptive move by the Egyptian regime" ahead of elections for the upper house of parliament due in April in which the Brotherhood is widely expected to take part.
Abdel Gelil el-Sharnoubi, the editor of the groups's website, said those arrested were mostly members who were expected to stand in the elections as assistants to the group's legislators.
El-Sharnoubi said the group had not yet chosen its candidates "but the government targeted figures who are popular in their provinces and are expected to run in the elections."
The website said many professionals were also held, including doctors, engineers and teachers.
The arrests came as US-based Human Rights Watch called on Egypt on Thursday to free hundreds of Brotherhood members it said were detained "solely for exercising their rights to freedom of expression and association".
Sarah Leah Whitson, Middle East director for the organisation, said: "By trying to crush Egypt's largest opposition movement, the government has shown once again that it cannot tolerate any criticism."
Essam al-Ariyan, a Muslim Brotherhood leader, told Al Jazeera: "From this [arrest of members] we can sum up an important reality that people's freedom and rights are sharply regressing.
"The government wants to force out any power that is popular and active and just keep those oppositions that would support it or would not seriously oppose it. The reform process itself is being targeted."
The latest arrests came a week after Egypt referred 40 members of the group including Khairat el-Shatir, the third-in-command, for trial in military courts, where verdicts are often issued quickly and cannot be appealed.
Those 40 men, who face terrorism and money-laundering charges, will be the first Brotherhood members to have military trials since 2001.
The group said it was preparing for a tough legal response.
Egypt has stepped up its pressure on the Brotherhood since the group's strong showing in 2005 elections for the lower house of parliament, in which the Brotherhood won nearly one-fifth of seats with members running as independents to bypass a ban.
Since the elections several hundred Brotherhood members have been arrested and the group's finances have been targeted, with authorities detaining financiers, freezing assets and raiding businesses.
Diya Rashwan, an expert on Islamist groups, told Al Jazeera from Cairo: "In line with the recent constitutional amendment, the Egyptian government is trying to exclude the Muslim Brotherhood from politics in the future. ... This is a critical moment for both the government and the Brotherhood."
On the question of whether condemnations of the arrests by international human-rights organisations would have any effect on the Mubarak government, Rashwan said: "In the last 10 years, there have come many condemnations of the arrests of Muslim Brothers and other political party leaders, but no reaction has come from the government."