Balivanich is said to have had long running problems with the smell
The Ministry of Defence said it was dealing with the cause of complaints about a bad smell linked to a sewage plant on land it owns.
Islanders on Benbecula in the Western Isles said a broken outflow pipe had led to waste leaking onto a beach at Balivanich.
Local councillor Martin Taylor is concerned the leak poses a health risk to people living nearby.
The MoD said the pipeline had been repeatedly damaged by storms.
It is in discussions with Scottish Water about resolving the problem which has seen treated waste leak onto the beach.
The base is run on the ministry's behalf by defence and security company QinetiQ, while Scottish Water supplies it with water under the MoD's Project Aquatrine water and waste water initiative.
Mr Taylor said the smell had been the subject of previous reports and reviews, but the problem persisted.
The councillor added: "There is a lot of concern locally because if you can smell this stuff there must be a bacteria in the air.
"Also there is concern about anybody going fishing on the beach or gathering shellfish.
"I have heard lots of people complaining about the smell and clearly it will put people off if that stuff is hanging about in the air. Primarily I am concerned about the people of Balivanich."
MoD said it was working with the Scottish Environmental Protection Agency (Sepa) to resolve the problem.
A spokesman said: ''We are aware of damage to the pipe at a MOD base in Benbecula which is causing sewage to discharge onto the beach.
"Water supply to the MoD occupied areas of Benbecula is supplied by Scottish Water via MoD's water and wastewater initiative Aquatrine. Aquatrine also looks after the waste water for the MoD occupied areas."
Stuart Baird, Sepa's unit manager for the Western Isles, said the organisation had been working with the ministry for some time on the problem.
He said: "Sepa has received complaints about the sewage discharge from the Ministry of Defence base at Balivanich, Benbecula, onto the nearby beach and has investigated these.
"The base has a septic tank and a licence which permits discharge of sewage effluent from it to deep water, but problems have been caused by damage to the pipe which means the discharge is not currently being made as far out to sea as is required by the licence."
Mr Baird added: "Sepa has been working with the MoD for some time to find an appropriate, practical and long term solution to the problem and is expecting a resolution to this matter in the near future."
Former military sites on Benbecula include Royal Artillery and RAF ranges.
Down the coast from Balivanich is Poll na Crann beach, also known as Stinky Bay because of the fermenting seaweed found there.