The incident was described by the government as a foiled attack by coup plotters who had crossed the border from Ghana and attacked Tokoin barracks in the capital.
The government has imposed a dusk to dawn curfew on the capital and closed the country's land borders. Residents were also asked to stay at home during the day.
Fighting broke out around the Tokoin camp on Wednesday evening. The government said the attackers had crossed the border by motorbike, taxi and in a four-wheel- drive vehicle. Officials said security forces had intercepted the attackers' radio conversations in English and the local Ewe language.
This version has been challenged by opposition politicians who yesterday accused the government of covering up a fight within the army and said the government was purging officers from the Ewe group. Ghana has also denied any involvement in the incident. A flare-up last year, explained in a similar way by the government, turned out to be a purge within the army.
President Eyadema is a Kabye, from the north, and the opposition is led in the capital by the coastal Ewe people who also live in neighbouring Ghana.
The government spokesman also announced the postponement of the parliamentary elections, due on 23 January, for two weeks, though it said this had nothing to do with the shooting incident. Togo came close to becoming a democracy until the former military dictator won a rigged election last August. In the enthusiasm for multi-party democracy which swept Africa two years agol, Togo produced one of the few recorded examples of unarmed crowds forcing the military back to barracks and holding a national convention to discuss the future of the country.
President Eyadema, who has ruled since 1967, was forced to cede many of their demands and hold an election but the army continued to hold ultimate power. The main electoral challenger, Gilchrist Olympio, barely survived an assassination attempt and was then banned from standing on a technicality.
The opposition parties boycotted the election but Mr Eyadema outmanoeuvred them. A farcical election went ahead and was accepted by Togo's closest western ally, France, the former colonial power.
Earlier this week about 40 French soldiers arrived in Lome on on what the government described as 'electoral observation mission'.