Eleven Egyptians, including people who worked in the Emirates for more than 20 years as doctors and engineers, were arrested, local media reported.
The al-Khaleej newspaper said the group had been under investigation for years and said cell members had established commercial companies to support their activities and allegedly illegally transferred large sums of cash to members in Egypt.
They were allegedly involved in compiling classified military information on the Emirates' army, the newspaper said.
Cell members allegedly conducted training sessions for new recruits and discussed ways to overthrow regimes in Arab countries.
"The Muslim Brotherhood saw the Arab Spring as an historic opportunity to leverage their political gains in Egypt and Tunisia to destabilize the current Arab governments, especially in the Gulf, to expand their power base and dominate societies," an unidentified analyst in the Persian Gulf told Gulf News.
"We want people to be calm so that in the end it does not backfire on relations between the two countries," Tamer Mansour, Egypt's ambassador to the United Arab Emirates told The National, a newspaper in Abu Dhabi. Mansour said relatives of three doctors arrested had contacted him.