Mike Casey, general manager of the company, said he was “disappointed” by the report from the Care Quality Commission and that some changes were not “recognised” by the CQC.
Inspectors raised concerns about the service including infection control, staff training and leadership.
But Mr Casey assured councillors on the Health Scrutiny Panel for Lincolnshire that a plan was in place to improve the service.
“We are committed to ensuring our staff are able to provide the highest standard of service to our patients, and we are confident that we are making the improvements needed to achieve this,” he said.
“The CQC have rated Thames as good for the care we provide, and the report states that feedback from patients confirmed that our staff treated them well and with kindness.
“We have made significant improvements since 2018, some of which we were disappointed have not been fully recognised within the report.
“We have also been having regular meetings with NHS England and CCGs to update them on the significant progress we have made.”
But chair of the panel, Councillor Carl Macey, said the service was not “fit for purpose”.
“We have seen over the last 12 months now that the key performance indicators have not moved very far,” he said.
“In fact, they are just as bad as 10 months ago when we were told they were turning things around and that would benefit the residents of Lincolnshire.
“Unfortunately that has not happened.”
Thames has come under fire recently for its contract performance in Lincolnshire.
The health scrutiny panel for Lincolnshire passed a vote of “no confidence” in the service back in December 2018.
However bosses at Lincolnshire West CCG, which commisions the non-emergency patient transport service, said it was not the “right time” to terminate the contract.