Its Asia division deputy director Phil Robertson said that it was evident that Putrajaya thought that Pakatan would break up if Anwar was jailed.
"The government thinks that Pakatan will collapse if Anwar is jailed," he told The Malaysian Insider at the Palace of Justice, Putrajaya, today.
"So it is up to them to prove Putrajaya wrong."
The apex court rejected Anwar's appeal against the guilty conviction by the Court of Appeal over a sodomy complaint by his former aide, Mohd Saiful Bukhari Azlan in 2008.
Robertson said Putrajaya, led by Prime Minister Datuk Seri Najib Razak, had persisted in Anwar's prosecution in what he described as a politically motivated move.
"The government has persisted in its politically motivated prosecution of opposition leader Anwar Ibrahim at the expense of democratic freedoms and the rights to non-discrimination and privacy for all Malaysians.
“Allowing this travesty of justice to stand will further undermine respect for rights and democracy in Malaysia," he said in a statement.
Anwar, the PKR de facto leader, will lose his Permatang Pauh parliamentary seat as the law bars anyone jailed for more than a year or fined more than RM2,000 from serving as a lawmaker.