Kerry last raised the matter with Putin on March 24 this year, a State Department official said.
"He has raised it with President Putin," State Department spokeswoman Elizabeth Trudeau told a news briefing earlier, adding: "We see an increase and we take it seriously."
Trudeau said harassment by Russian security agents and traffic police had been an issue over the past two years, but did not give details of incidents nor why it was raised with Putin.
Other Western embassies had reported the same behavior toward their diplomats stationed in Moscow, Trudeau added.
Washington stripped five of the six Russian honorary consuls of credentials in January to retaliate for harassment of its diplomats in Moscow. In response, Russia's Foreign Ministry accused the United States of provoking Russian diplomats in the United States and elsewhere.
Honorary consuls are typically U.S. citizens or green card holders who perform consular services on behalf of a foreign government, a U.S. official said, saying the five were located in California, Florida, Minnesota, Utah and Puerto Rico.
Asked whether harassment of U.S. diplomats occurred only in Moscow, Trudeau said: "We can't rule out such harassment that could occur elsewhere. I just don't have specifics on other countries."
Despite cooperation between Moscow and Washington on the Iran nuclear deal, tensions between the two countries have escalated since Russia annexed the Crimean Peninsula from Ukraine in 2014 and Moscow's increasing backing for Syrian President Bashar al-Assad.