The GMB union has accused the BII of "washing its hands" of a Peak District tenant's dispute with Punch Taverns.
It claims that tenant David Mountford was misled over £180,000 investment, lied to and badly treated by Punch Taverns managers.
Mountford, who runs the Rising Sun in Middleton in Derbyshire, wrote to the British Institute of Innkeepers to complain of his treatment by Punch over a period of more than two years since March 2007.
In May this year, Mountford asked the BII to investigate his complaint and if they uphold it to strip Punch Taverns of membership as a fit organisation to operate in the pub industry.
The GMB has accused the BII of being "disingenuous" in giving the impression it has the power to help tenants resolve disputes with their pubco.
BII chief executive Neil Robertson said: "It is not our policy to comment on specific enquiries, especially while they are still ongoing.
"On the occasions that we receive reports of a potential code breach, we take the matter very seriously and investigate each one on a case by case basis, as we are doing at present with this particular complaint.
"If we find there to be a breach, we pursue this with the pub company until a mutually satisfactory resolution has been achieved and, whilst we don't widely advertise the fact, we consistently get good outcomes for our members."
Benchmarking
He added: "BII created the Benchmarking and Accreditation Services (BIIBAS) scheme in early 2007 to assess and independently benchmark the clarity of pub company codes for prospective and current leaseholders or tenants.
"We are currently in discussion with the pub companies regarding proposals to extend the scope and ambition of the scheme, however, at this time each code is examined and assessed for transparency and clarity.
"Therefore, some issues flagged up by Mr Mountford and GMB go beyond the remit of BIIBAS.
"They do, however, underline the importance of an industry mediation scheme, which, as we all know, is being introduced in response to the BEC inquiry report and will continue to drive up standards in business management. It is this mediation process that will resolve complicated issues such as the one between Mr Mountford and Punch.
"In any industry things will go wrong from time to time and it is important to have processes and procedures in place to guide and support both parties to a resolution when this happens. This is why BII established the BIIBAS scheme and has actively encouraged the creation of the Pubs Independent Rent Review Scheme (PIRRS) and other mechanisms.
"BII will continue to encourage pubcos to compete for tenants on quality, as this is critical to business success, and we see increasing evidence that they are doing this."
Disingenuous
GMB national organiser Martin Smith said: "BII is being disingenuous in giving the impression that they have some agreed procedures to help individual tenants resolve specific disputes with pubcos.
"It is now clear that there are no such procedures. Neither has BII the ability to sanction Punch by stripping them of membership.
"BII is washing its hands of resolving Dave Mountford's complaints against Punch and disguising this by seeking to set up more talking shops and to spin that positive changes are underway in this industry.
"It is time for pub tenants to call time on fake mediation bodies and other talking shops like BII."
Punch Taverns said it "refutes" the "unsubstantiated" claims made by Mountford.