The payments totalling about $60,000 came in the form of 68 separate deposits and Thompson used the money for herself.
Last year the trust was suspended for 60 days after a Ministry of Social Development (MSD) review revealed financial concerns.
It was later closed when police launched a separate inquiry over the concerns.
The SFO investigation into financial management practices came to a head this month when trustees for the service applied to liquidate the trust.
A charitable trust based in Hamilton, RWSS delivered social services in the Waikato region.
It had received funding from the Ministry of Social Development, Ministry of Health, Ministry of Justice, Department of Corrections and Waikato District Health Board since 2008 for the provision of those services.
They included providing budgeting advice, whanau support, non-violence programmes and youth justice services under the Government's Whanau Ora scheme.
Thompson's charges included one of obtaining by deception and 67 of theft in a special relationship.
SFO director Julie Read said Thompson had control over the Raukura funds and knew the terms under which she was allowed to deal with that money.
"She intentionally departed from those terms to conduct this activity for her own personal benefit."
Thompson will be sentenced in the Hamilton District Court on June 1.
