Badawi's sister went to the Jeddah court Monday to follow up on a local media report that an appeal was denied. There, she received confirmation from the court that the sentence was upheld.
Badawi who has been imprisoned since 2012, was charged with violating Saudi Arabia's information technology law and insulting Islam through his website "Saudi Arabian Liberals."
The lashings are to be carried out 50 lashes at a time, 20 weeks in a row. Badawi endured the first 50 of the 1,000 lashes stoically in January, arching his back in pain. The flogging provoked an outcry from human rights groups and U.S. officials.
"Publicly lashing a peaceful activist merely for expressing his ideas sends an ugly message of intolerance," Human Rights Watch said at the time.
And Said Boumedouha, Amnesty International's deputy director for the Middle East, called for Badawi's immediate release.
"Raif Badawi is a prisoner of conscience; his only 'crime' was to exercise his right to freedom of expression by setting up a website for public discussion," Boumedouha said in a statement.
In a statement posted on the Amnesty website, Badawi's wife, Ensaf Haidar, called for the sentence to be lifted.
"Raif told me he is in a lot of pain," Haidar said. "He said that when he was being flogged he took the pain silently and rose above it, so that history will know that he did not react to their punishment. His health is poor and he cannot take another round of lashes."
U.S. officials have called on Saudi officials to withdraw the sentence and review Badawi's case.
On his "Saudi Arabian Liberals" site, Badawi, hosted political debates and advocated secularism, which he said "respects everyone and does not offend anyone."
Amnesty reported that eight days after the initial flogging, doctors determined that Badawi had not healed sufficiently to be flogged for the second time. The lashes have been postponed at least three times.
"A medical committee of around eight doctors carried out a series of tests on Raif on 21 January at a Jeddah hospital, and found that wounds sustained from the 50 lashes dealt to him by Saudi officials nearly a fortnight before hadn't healed enough for him to be lashed again without serious risk to Raif's health," the rights group said.