Badawi received the first 50 lashes of his sentence outside a mosque in the Red Sea city of Jeddah on January 9, and subsequent rounds of punishment were postponed on medical grounds.
In a statement, a foreign ministry spokesman "strongly denounced the media campaign around the case of Raef Badawi", and deplored criticism of the judiciary.
"The kingdom does not accept any form of interference in its internal affairs and rejects... the attack on the independence of its justice system," the official SPA news agency quoted the spokesman as saying.
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The case of Badawi, 31, has sparked worldwide outrage and criticism from the United Nations, United States, the European Union, Canada and others.
Badawi co-founded the Saudi Liberal Network Internet discussion group.
He was arrested in June 2012 under cybercrime provisions, and a judge ordered the website shut after it criticised Saudi Arabia's notorious religious police.
On Saturday, the ministry spokesman said "the kingdom accepts no attack in the name of human rights, as its constitution is based on sharia (Islamic law) that guarantees human rights".
He denounced attempts by "some international parties", that he did not name, to politicise the issue of human rights by "selectively attacking the sovereign rights of states".