In a statement, national police said it had arrested Juan Holmann Chamorro for customs fraud, as well as laundering money, property and assets, adding to a mounting crackdown against the paper and other critics of the Ortega administration.
Representatives for the paper declined to comment.
The British government on Saturday added to the growing condemnation of Ortega and his wife, Vice President Rosario Murillo, saying the pair were resorting to authoritarian methods to stifle opposition and free elections later this year.
A day before Friday's raid on La Prensa, the paper said it was no longer able to put out a print edition because the government was withholding paper from it. read more
On Friday night, Ortega had accused the newspaper of "lies, slander, defamation, money laundering and not paying taxes."
His government's attacks against the opposition and critics have left Ortega increasingly isolated internationally.
Ortega, a former Marxist guerrilla and erstwhile Cold War antagonist of the United States, is seeking to secure a fourth consecutive term in power in elections due in November.
In a statement, British Foreign Office Minister Zac Goldsmith accused the Ortega administration of an "abuse of power" to sideline opponents and prevent a fair vote.
"With opposition figures detained, including seven potential presidential candidates, and a crackdown of fundamental rights and freedoms, November's elections will lack credibility," he said. "This increasing authoritarianism must end."
Goldsmith did not mention La Prensa.
La Prensa is controlled by the Chamorro family, some of whom are longtime adversaries of Ortega. Following the arrest of the general manager, four members of the family are now in custody. Reporting by Ismael Lopez; Editing by Daniel Wallis and Christopher Cushing