The kingdom "has expressed strong disbelief and condemnation" at statements about the case of Raif Badawi, the Saudi Press Agency said, citing an official source at the foreign ministry.
Rights groups fear he could be flogged again as soon as tomorrow, despite appeals from the United States, European Union and France for his sentence to be rescinded.
Swedish Foreign Minister Margot Wallstrom on Tuesday accused Saudi Arabia of handing Badawi a "medieval" punishment.
Saudi Arabia's judiciary "enjoys independence and the kingdom does not accept any interference in its judiciary and internal affairs from any party," the Saudi foreign ministry source said.
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But Badawi's wife said last Sunday that the kingdom's supreme court had upheld that verdict.
"This is a final decision that is irrevocable," Ensaf Haidar told AFP in a telephone interview from Canada. "This decision has shocked me."
She and the couple's three children have been granted asylum in Quebec.
Badawi received the first 50 lashes outside a mosque in the Red Sea city of Jeddah on January 9. Subsequent rounds of punishment were postponed.
"I was optimistic that the advent of (the Muslim fasting month of) Ramadan and the arrival of a new king would bring a pardon for the prisoners of conscience, including my husband," Haidar said, referring to King Salman who acceded to the throne in January.
He was arrested in June 2012 under cyber-crime provisions and a judge ordered the website shut after it criticised Saudi Arabia's religious police.
Badawi's lawyer, Walid Abulkhair, who is also a rights activist, is behind bars as well.
Badawi and Abulkhair have been nominated for this year's Nobel Peace Prize by Norwegian member of parliament Karin Andersen.