Brussels announced the expulsion of Nicaragua's top diplomatic representative as a tit-for-tat move.
Nicaragua's foreign ministry says the decision was taken because the "interventionist and neo-colonial" European country had "offended and keeps offending Nicaraguan families".
Government alleged financial crimes were committed through a press freedom training and defence centre that Chamorro directed for 20 years and which has since been shuttered.
Two opposition politicians punished for participating in violent protests last year against President Daniel Ortega that left 325 people dead, their lawyer says.
Nicaraguan President Daniel Ortega is facing the biggest challenge to his leadership since returning to power in 2007. More than 280 people have been killed since April, but he has so far resisted demands to resign and hold early elections.
The latest deaths over a 24-hour period has raised the total death toll in protests against the regime of President Daniel Ortega to 83 killed since April 18.
These deaths, confirmed by the local Red Cross, are the latest in a wave of protests against social security reforms that have rocked this Central American nation.
Protests over pension reforms subside in the Central American country after President Daniel Ortega makes a series of concessions, including freeing dozens of arrested protesters, lifting curbs on independent media and calling for dialogue.
Nicaragua's decision to enter the pact means only two countries will now be outside it – the US and war-torn Syria.
Tropical Storm Nate pummeled Central America with heavy rain while heading toward Mexico's Caribbean resorts and the US Gulf Coast where it could strike as a hurricane this weekend.
Storm Otto smashed into southeastern Nicaragua on Thursday as a category 2 hurricane before crossing into Costa Rica but weakened rapidly and became a tropical storm by early Friday.
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