On Austrian national Ö1 radio on Friday, he urged Defence Minister Gerald Klug of the Social Democrats (SPÖ) to present reform plans, so the army would not be "starved out".
The SPÖ reacted with annoyance, saying that as finance minister, Spindelegger was in charge of the budget.
The ÖVP leader then said that he did not want to criticise Klug, but he did expect plans by the autumn, so that the financial problems "which the army clearly had" could be eliminated with a reform in the next few years.
Klug said that the finance minister knew very well what the situation was like, since Spindelegger's ministry cut funds for the army earlier this year.
"We have reached the bottom of the barrel, there are no more reserves," said Klug on Friday, adding that he would be presenting reform plans in the autumn anyway.
He was supported by head of the general staff, General Othmar Commenda, who said he was "stunned" by Spindelegger's comments.
Spindelegger's previous target for reforms was the Austrian state railways.