Relations soured between the two countries late last month after Peru claimed Chile paid three members of the Peruvian navy to spy on their own nation.
Peru's foreign ministry yesterday announced the withdrawal of the ambassador in a statement, saying he would not return until Chile provided necessary assurances over the incident.
Lima recalled Ambassador Fernando Rojas Samanez on February 20 after it made the claims against Chile and detained the alleged spies.
In a first protest note, Peru claimed the military members were paid for spying by Chile between 2005 and 2012.
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In a second letter of protest issued yesterday, Peru said it "reiterates its firm rejection and deep concern" over the "actions of espionage by Chile."
"This is Peru's sovereign decision to make" if it so chooses, Chile's Foreign Minister Heraldo Munoz said.
"We cannot comment (about Peru's diplomatic notes). After reviewing them, we will comment at the appropriate time.