National police commissioner Bheki Cele said Mr Wright had "admitted to harbouring and interviewing Mr Pavlos Joseph at a time when the police were searching for the latter in order to effect anarrest".
Chile's Supreme Court ruled that he could be prosecuted at home for disappearances, but the Appeals Court quashed anarrestorder against him on technical grounds.
Thursday's order to arrest him was an unprecedented move against a former army chief who ruled the country for almost a decade, the BBC's Orla Guerin in Islamabad says.
But the committee did not support making legal aid free to all for applications to a civil court for an interdict with a power of arrest, or a non-harassment order, where domestic abuse was involved.