Thomson was arrested in Havelock North early on Sunday following a complaint of assault on a female, police spokesman Grant Ogilvie told Hawkes Bay Today yesterday.
Thomson becomes the third Highlanders player to face court charges in an awful year on and off the field for the franchise.
Halfback and fellow All Black Jimmy Cowan was involved in three incidents. He was convicted of two disorderly behaviour charges and a third was dropped.
Otago and Highlanders winger Lucky Mulipola was convicted of assault in Dunedin in April, and he was also convicted on two driving charges.
Both Cowan and Mulipola were given alcohol bans by the New Zealand Rugby Union, their primary employer.
It is not known whether the Thomson incident was alcohol-related, nor are there any details of the alleged assault.
Thomson is on holiday, having returned from the All Blacks' Grand Slam tour, and is believed to have been visiting friends in Hawkes Bay.
Both the Otago Rugby Football Union and the NZRU are declining to elaborate on the Thomson incident or talk of disciplinary action until the court case is settled.
ORFU chief executive Richard Reid said he would not comment as the matter was before the court.
New Zealand Rugby Union professional rugby manager Neil Sorenson was aware of the incident, but said it would be inappropriate to make further comment as it was a police matter.
There have been two instances in recent times of a current All Black being charged with assault. Two years ago, Sione Lauaki admitted a charge of assaulting a security officer in Hamilton and was offered diversion.
In April last year, Sitiveni Sivivatu admitted a charge of assaulting his wife but was discharged without conviction.
Both players subsequently played for the All Blacks.
Thomson's arrest spoiled an extraordinary year in which he finally established himself as a regular Highlander and played nine tests for the All Blacks.
