Egypt put two former top ministers on trial on Sunday, cracking down on corruption that led to Mubarak's ouster.
Private equity firm Citadel Capital, tumbled 9.4 percent after Egypt's public prosecutor ordered that Chairman Ahmed Heikal be banned from travel pending a probe into corruption allegations.
"Uncertainty prevails," said Youssef Kamal of Naeem brokerage. "Unfortunately, all companies are becoming suspicious from an investor's point of view."
The index closed 3.2 percent down at 4,956 points, its lowest since March 24.
Saudi Arabia's Tadawul All-Share Index (TASI) edged up slightly to close at 6,533.34 points, with banks and Etihad Etisalat (Mobily) supporting on first-quarter earnings. The stock market turnover exceeded SR5 billion on Monday.
Mobily rose 0.5 percent after reporting a 40 percent growth in first-quarter net profit late Sunday, coming in just below the average forecast by analysts polled by Reuters.
Al-Rajhi Bank and Banque Saudi Fransi rose 0.3 and 0.9 percent respectively.
"Investors need to keep in mind going forward that there is already a lot of positive news priced into the market at these levels," said Amro Halwani, a senior trader at Shuaa Capital in Riyadh.
After market close, Saudi Basic Industries Corp. (SABIC) reported first-quarter results with net profit rising 42 percent, widely beating forecasts.
Qatar's index fell 1 percent to 8,645 points to a two-week low, with Qatar Gas Transport Co. (Nakilat) weighing after paying out dividend. Nakilat fell 5.2 percent, while losses were seen across the board.
"It's healthy for the market to be down again," said Hani Girgis, assistant chief dealer at Dlala brokerage.
UAE markets edged to a higher close, as investor sentiment is upbeat on a combination of quarterly earnings and the country's perceived safe haven status.
Investors however are doubting UAE's likelihood of inclusion in MSCI emerging market index.
"It is hard to argue that a market that trades $100 million a day and really has only 10 to 15 liquid investable names should be included in the MSCI," said Robert McKinnon, ASAS Capital chief investment officer.
Dubai's index rose 0.3 percent to 1,653 points and sits on a 14-week high and Abu Dhabi's benchmark climbed 0.4 percent to 2,709 points — a nine-week high.
Kuwait's index rose 0.5 percent to 6,375 points as investor fears settled after the death of Kharafi Group's chairman on Sunday that triggered a sell-off. The benchmark ended 0.5 percent higher.
Until first-quarter earnings season ends, Kuwait's will be "a volatile within reason market," said Jasem Al-Zeraei, head of sales at National Bank of Kuwait.
The Omani index slipped 0.1 percent to 6,397 points. The Bahraini measure shed 0.06 percent to 1,403 points.
