The 18-hour general strike was called from Friday midnight by the Coordination Committee (Corcom) of the six outlawed underground organisations.
All educational institutes, government offices, shops and business establishments remained shut and vehicles were off the roads in response to the shutdown call.
Security was tightened in all vulnerable areas as officials feared an outbreak of violence.
Inter-state buses and trucks were stranded beyond Manipur's borders.
A public convention held recently in Imphal declared the agreement as null and void, saying Manipur had an elected assembly and that the king was merely a constitutional head at the time of the merger.
The king, according to the Corcom, had no power to sign such documents without approval from the elected house.
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