"I am alarmed that the Supreme Court of the Maldives is interfering excessively in the presidential elections, and in so doing is subverting the democratic process and violating the right of Maldivians to freely elect their representatives," Pillay said in a statement.
The Supreme Court nullified the first round of the presidential election on September 7 after a candidate complained of irregularities in the balloting.
However, Pillay noted that the general conclusions by national and international observers were that the "election was free and fair".
"It was on this basis that police prevented the Elections Commission from carrying out its plan to re-run the election on October 19."
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Several parties, including the Maldivian Democratic Party of former president Mohamed Nasheed, have condemned the blocking of the polls, which sparked protests in the country.
Pillay called for the election to be held, saying: "All parties should seize this opportunity to restore the credibility of the democratic process.
"Whoever wins the election should embark on fundamental reforms to the judiciary to safeguard Maldives' progress in democracy and rule of law."