Intelligent Giving has said it will reassess Lepra's use of the accolade once it has heard the results of three upcoming employment tribunal cases against the charity.
The allegations, posted on Lepra's page of Intelligent Giving, include a claim that the charity made misleading statements to one of its funders, the Guernsey Overseas Aid Commission.
One ex-employee, Doug Frame, has a tribunal hearing in December. He told Third Sector his case would be that Lepra asked staff to write a report to the funder falsely stating that all the commission's funding to the charity had been spent.
Third Sector has seen an email in which Rene Vargas, director of programmes at the charity, asks a former employee to write the report and later decide how to spend the money. It reads: "First produce the report and later on ... plan about the resources left and the work which needs to be done."
In this case, £17,330 for a project to eliminate lymphatic filariasis had been left unspent and was instead earmarked to cover internal costs.
Ian Gibbons, finance director of Lepra, said: "All reports that have been made to the Guernsey and Jersey Overseas Aid Commissions have been accepted by these agencies on their submission and no concerns relating to these have been raised with Lepra.
"Lepra is a very well managed, reputable charity that finds itself facing untrue and unfounded allegations of impropriety from disgruntled ex-employees, who are bringing claims against the organisation in the employment tribunal.
"Lepra vigorously denies any wrongdoing and believes that these allegations are being made recklessly or maliciously with the intention of causing damage to the organisation."
A spokeswoman for the Charity Commission confirmed that it had received two complaints about Lepra's administration and governance. "We are currently considering these concerns to determine what action, if any, might be appropriate, but this is not a formal inquiry," she said. "We will be considering the outcomes of the tribunals to see if they raise issues for us."
Lepra was found to have unfairly dismissed Rokunuz Zaman, its former Bangladesh programmes officer, in a fourth tribunal case that ended last month (Third Sector, 25 July).