She said that because of the changes, indigenous Queenslanders have been forced to wait up to nine months in prison before seeing a lawyer.
In a meeting of Australia's attorneys-general in Darwin on Tuesday and Wednesday, Ms Lavarch will call on Federal Attorney-General Phillip Ruddock to reassess the overhaul.
Last year, Mr Ruddock presided over the restructuring of Queensland's legal aid services, under which 11 services were reduced to two, servicing the state's north and south separately.
It also resulted in a 10 percent funding reduction and a wider legal scope, taking in civil and family law in addition to its existing criminal law focus.
But Ms Lavarch argues that while the southern Queensland service appears to be operating quite well, the state’s service in the was not coping with the high volume of work.
Most of the Queensland's indigenous community lives in northern parts of the state.
"There are difficulties in the operation of that service," Ms Lavarch said.
"We have had reported to us situations where people are held in custody for some months that have not yet had the opportunity to speak to a lawyer."
"What it means is they are not getting experienced legal representation which may well mean they are not having their case properly put before the court and they may be pleading guilty when they have a defence," Ms Lavarch said.
Ms Lavarch said she didn’t know how this affected indigenous incarceration rates.
She said the restructure had resulted in cost shifting from the commonwealth to the state government, with the state's legal aid system forced to take on the extra caseload.
Just one matter involving legal representation over the Palm Island riots had already cost the state about $1.1 million.
Ms Lavarch said she would ask Mr Ruddock to review the restructure before similar mistakes were made in other states.
To date, only Queensland, Western Australia and the Northern Territory have undergone the restructure.