The Central Otago District Council spent $80,000 refurbishing the toilets and was disappointed at the damage caused by the fire between 12.30am and 1am on Monday.
Council property and facilities manager Mike Kerr said toilet paper rolls in the men's toilet were set alight, damaging the toilet partition and causing extensive smoke damage.
The toilets were closed yesterday so a cleaning crew, an electrician and contractors could check wiring and repair the damage.
The council had security cameras mounted on nearby buildings and a door counter which it hoped would help police find the offenders.
Alexandra Police had released CCTV images from outside the toilet block in the hope of identifying two males, Constable Rowan Williams said.
''It is fortunate that the fire did not take hold and cause more significant damage or pose risk to life. It appeared one of the pair was wearing a cast on his right forearm. If you recognise the two males in the photos make contact with police,'' Const Williams said