The ARU's chief operating officer has resigned in a blow that threatens to further delay the removal of an Australian Super Rugby side.

Rob Clarke announced his sudden resignation to staff on Thursday.

The former Melbourne Rebels chief executive has been a central figure in the process of either the Rebels or Western Force being cut from Super Rugby as part of SANZAAR's restructuring of the competition in 2018.

Clarke had been working closely with ARU boss Bill Pulver in the delicate operation, as well as liaising with the Rebels and Force since the two franchises were confirmed last month as being in the firing line.

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It was hoped that the naming of the two South African franchises and one Australian club to go would take place at a SANZAAR meeting in Tokyo next Wednesday.

But the saga shows no sign of ending.

Both the Force and Rebels maintain the ARU has no right to remove their teams in SANZAAR's downsizing to a 15-team tournament, with WA Rugby having commenced legal action and the Melbourne club seeking compensation.

Clarke, who endured criticism from the West Australian franchise in recent weeks around his former links to the Rebels and Brumbies, had been considered a future CEO of the embattled national body.

The former advertising executive returned to the ARU in 2014 as general manager of professional rugby, operations and marketing.

His elevation to chief operating officer in 2016 was his second stint in the role.