In the newly discovered boxes, many uncounted ballots from different precincts were found mixed together “in the wrong place, badly organized,” Mr. Rosado said. But he stressed that none of them had left the elections vault, and their discovery underscored the transparency of the process.
It was unclear how many votes the boxes contained, he said at a news conference on Tuesday.
“There are cases that have three ballots, there are cases that have 500,” he said. On Wednesday morning, he told WKAQ-580 AM radio that it could be between 3,000 and 4,000 votes.
“Trust in the transparency of the process,” Mr. Rosado said. “Every vote will be counted.”
“Asking that of the country is absurd,” Carmen Yulín Cruz, the outgoing mayor of San Juan, tweeted in response.
Critics blamed the ruling pro-statehood party, which this year changed the electoral law in fundamental ways that gave Mr. Rosado’s party more control over elections. The New Progressive Party’s representative on the elections council, Héctor J. Sánchez, insisted that the government’s party wanted every last vote counted.
All of the opposition parties had agreed on Saturday to stop counting votes, he argued, despite lingering questions about ballots in some races that appeared to be missing.
In Puerto Rico, each race is voted on a different ballot, and there were discrepancies in the number of votes cast in some areas.
The ballots in the extra boxes were not really newly discovered, Mr. Sánchez claimed, but had been tagged with some kind of problem during the initial count and were set aside to be reconciled during the tally certification process.