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The move by Robert T Stevens came on the first day of the hearings into communist activity in the US army.
Mr Stevens said he would speak on behalf of the army provided the session was in public.
His announcement came after a former army major summonsed by Senator McCarthy - head of the Senate's Permanent Investigations sub-committee - refused to answer questions.
Irving Peress, now a dentist, took advantage of the Fifth Amendment in the US' Constitution - the right to avoid self-incrimination - to justify his silence.
Mr Peress cited his honourable discharge from the army as proof of his "honest and loyal service" to his country.
Senator McCarthy has accused Mr Peress of communist activities at an army camp and has demanded that army authorities revoke his honourable discharge and court martial him.
The Wisconsin senator has also called for a list of all officers and civilians who had anything to do with Mr Peress' promotion and honourable discharge.
"Either the army will give the names of men coddling Communists or we will take it before the Senate," he said.
However, Mr Steven's stand makes it unlikely a list will be forthcoming.
It is a rare challenge to the controversial senator who was virtually unknown before he took up the cause of rooting out Communists four years ago.
In a speech in West Virginia in February 1950 Mr McCarthy claimed to have the names of 205 "card-carrying Communists" in the State Department.
However, he later scaled down the list to 57 and was willing to name only four of them.
His critics say he has never produced real evidence to back up his claims and accuse him of "witch hunts" which have often destroyed the careers of those accused.
But in March 1951 Julius and Ethel Rosenberg were convicted for passing atomic secrets to the Russians and this helped fuel popular support for his campaign.
Joseph McCarthy's committee works parallel to the House of Representatives' Un-American Activities Committee (HUAC).
In 1947 the HUAC's high-profile investigation of the entertainment industry led to prison sentences for 10 Hollywood writers and directors who refused to answer questions and "blacklisting" for hundreds more.
The "Army-McCarthy" hearings proved to be Joseph McCarthy's undoing.
He found himself under investigation after army officials alleged he had tried to obtain preferential treatment for a former aide drafted into the army.
A much-publicised investigation by the Senate ended inconclusively.
But in December 1954 the Senate voted to censure Mr McCarthy for abusing his power as a senator - only the fourth time in history a senator had received such a public mark of disapproval.
His career never recovered and he died in obscurity from an alcohol-related illness in 1957 aged 48.
However his name lives on in the term "McCarthyism" defined by the American Heritage Dictionary as "the use of unfair investigatory or accusatory methods in order to suppress opposition".
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