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Nesirky said the UN secretary general planned to speak with President Mahinda Rajapakse "in the coming hours" about the case.
Sri Lanka said earlier Tuesday it would court martial Fonseka for conspiring against the government and sacked parliament to make way for snap polls.
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The Sri Lankan defense ministry said Fonseka, who was seized by troops at his office in Colombo on Monday, will face a court martial even though he quit in November following a rift with the president.
The opposition said Fonseka was "grabbed" by the military while he discussed plans to contest upcoming parliamentary polls with several senior party leaders who had backed his failed bid for the presidency last month.
The government said Fonseka had been "conspiring" with oppositio