Nine in 10 doctors, nurses and other front-line staff at St Helens and Knowsley Hospitals have had the flu jab, Public Health England figures reveal.
By the end of December 2018, 90% of front-line workers at the trust were vaccinated - the highest uptake in England.
NHS England is aiming for "near universal" coverage of the flu vaccine this winter among staff.
Of the 3,637 doctors, nurses, clinical staff and support workers at the trust with direct patient contact, 3,275 were vaccinated between September and December.
That's far higher than the national average of 66%, but 362 healthcare workers remain unvaccinated.
NHS bosses have now warned that staff refusing the vaccine could be banned from treating patients.
As a result, trusts are now required to submit data on how many of their staff refuse the jab.
St Helens and Knowsley Hospital Services NHS Trust reported that 139 staff turned down the jab - making up almost 40% of unvaccinated staff.
The other staff may not have been offered the vaccination yet.
Coverage at the trust has improved since the same period in 2017-18, when 85% of front-line staff were vaccinated.
This winter's uptake has varied considerably between trusts, with Oxleas Trust in south east London and the Birmingham and Solihull Mental Health Trust both reporting a vaccination rate of just 35%.
Dr Nick Scriven, president of the Society for Acute Medicine, said the variation in reported uptake was "disturbing".
He said: "I can see employers taking a firm stance with anyone who chooses not to be vaccinated and who then contracts influenza.
"The NHS workforce crisis is well-described, and anything that could further exacerbate that is to be avoided."
PHE medical director Professor Paul Cosford said: "Healthcare professionals have a responsibility to be vaccinated to protect themselves and their patients from flu.
"Front-line health and social care workers are at more risk of catching flu because of their contact with patients.
"They are also more likely to pass it on to their patients, many of whom will be at higher risk of serious complications of flu."
NHS England said staff have achieved a record level of uptake for the vaccine this winter.
Across the United Kingdom, there have been 1,684 hospital admissions and 102 deaths due to flu since October 2018.