The U.S. Embassy in Moscow, which reportedly was informed by Russia's foreign ministry of the incident, didn't respond to an emailed request for comment on the arrest.
Russian authorities have detained an American citizen over accusations of spying, according to Russia's Interfax news agency.
Russia's Tass news agency said Whelan faces between 10 and 20 years in jail if found guilty.
"Russia's obligations under the Vienna Convention require them to provide consular access".
Further details about the case could not be provided because of privacy concerns, the press officer said.
NASA announcement: New Horizons set for historic flyby TOMORROW
It is the second historic rendezvous for New Horizons , which zipped by Pluto in July 2015 on the first-ever flyby of that world. The first signal back to Earth should come about 10 hours after the flyby, around 9:45 am (1445 GMT).
Even before the allegations of election meddling, suspected spy incidents have been a frequent feature of U.S. -Russia relations. It happened just over a week after Russian President Vladimir Putin indicated he would not resort to retaliation, given the USA arrest of accused Russian agent Maria Butina.
Whelan's arrest follows the case of Maria Butina, a Russian gun rights activist who pleaded guilty in a US court earlier this month to acting as an illegal foreign agent leading up to and during the 2016 presidential election.
The Kremlin has denied that Butina is a Russian agent and has organized a social-media campaign to secure her release.
He also said that Ms. Butina had not been following any instructions from the Russian government or its agencies, and noted that she was fighting to avoid prison.
'We have read reports of the arrest in Moscow of Paul Whelan, our son & brother.
The United States levied new sanctions against Russian Federation for violating worldwide norms on December 19th.