Martin Couchman, the BHA deputy chief executive, has asked for clarification on both regulations from Home Office Minister Jeremy Browne.
"We have had many hours of discussion on the introduction of EMROs and the Late Night Levy with Home Office officials and it is disappointing that issues that were discussed at our meetings have largely been ignored in the final draft regulations.
"We are urging the Minister to clarify the regulations so that there is clear national framework that everybody can understand," Couchman said.
The Government is now in the early stages of implementation after both regulations came into force on 31 October. Neither measure is expected to be used until spring or summer next year.
The Late Night Levy gives local authorities the power to charge the cost of additional policing to licensed premises which remain open after midnight.
Meanwhile EMROs, originally introduced by the last Government, can be introduced by local authorities to restrict the sale of alcohol in certain areas, including hotels and restaurants, between midnight and six AM.
"During the original discussions it was agreed that resident hotel guests would be allowed to be served alcohol after midnight anywhere on the hotel’s premises, including the hotel's bars," Couchman said of the EMROs.
"However, the final draft of the regulations allows hotels to serve alcohol only via a mini-bar or room service.
"Guests who want to socialise will either have to retreat to one of their bedrooms to do so, with the result of noise and disturbance to other guests, or the law will create a farcical situation in which guests will go to their room to receive the alcohol and then head back to the bar to continue socialising," Couchman concluded.
The letter has been co-signed by Association of Leading Visitor Attractions, the British Beer and Pub Association (BBPA) and Business in Sport and Leisure.