The commissioner took the money from the pharmacy's account in September in the form of a practice payment adjustment, according to the Birmingham contractor, who wished to remain anonymous.
In two letters sent to the contractor last month, and seen by C+D, NHS England's regional team for West Midlands said "a sum" had been "deducted" from the pharmacy business's "payments for medicines use reviews...following identification of non-submission of the information governance toolkit".
"Non-submission of the annual toolkit is a breach of the terms of service and as such, could result in...witholdings of remuneration in respect of some or all respective advanced services provided," the regional team said.
The letters do not confirm the amounts involved, but the contractor told C+D that a total of "roughly £15,000" had been taken across "several branches" owned by their pharmacy business.
The contractor told C+D they had “robustly responded” when they had been alerted to the fine, and had threatened legal action against NHS England. The commissioner has since "backed-down" and so far had repaid two-thirds of the money, the contractor said.
The letters do confirm that, following a review, NHS England had decided to repay the sum.
However, the contractor added that NHS England has since “relaunched the assault” by reviewing three years’ worth of the pharmacy business's toolkit submissions.
Failure to follow "due process"
The Pharmaceutical Services Negotiating Committee (PSNC) told C+D in September it was aware that NHS England's West Midlands team had deducted money from "some" contractors “without following due process”.
“[We are] working with local pharmaceutical committees involved to manage the issue at a local level,” PSNC director of operations and support Gordon Hockey said.
NHS England responds
NHS England's West Midlands team would not confirm any details of the fine, but its head of primary care Richard Yeabsley said the commissioner "undertakes a range of activities to monitor contractors’ compliance against their terms of service".
"This includes a review of clinical governance systems which incorporate information governance," Mr Yeabsley said.
He confirmed that NHS England has engaged with LPCs "in respect to this matter, including the correspondence issued to contractors.”
What is the information governance toolkit?
Organisations that process patient information or provide services to the NHS are contractually required to publish an annual assessment.
Pharmacy contractors in England were expected to publish their toolkit submissions for 2015 by March 31 this year. The deadline for submitting this year's return is March 31, 2017.
More details about information governance submissions can be found on PSNC's website. Scotland, Wales and Northern Ireland are subject to different arrangements.