In a letter to defense committee leaders obtained by CNN, Mattis detailed the effects of a continuing resolution, which Congress frequently uses to keep the government funded at the previous year's spending levels.
President Donald Trump signed a three-month CR into law last week as part of a package that included aid for Hurricane Harvey relief and a three-month extension of the debt ceiling.
But the military objects to CRs because they aren't allowed to start new programs and are restricted in moving money between spending accounts.
"Long-term CRs impact the readiness of our forces and their equipment at a time when security threats are extraordinarily high," Mattis wrote. "The longer the CR, the greater the consequences for our force."
The military's objections to a continuing resolution are nothing new, as it's become standard for Congress to pass a CR to start the fiscal year, which begins in October, before approving a full-year appropriations bill later on.
But with the Trump administration seeking more than $50 billion in additional funding for the military compared to last year, a CR creates even more uncertainty for the Pentagon's budget this year.
Senate Armed Services chairman John McCain was one of 17 Republicans to vote against the spending package, and House Armed Services Chairman Mac Thornberry was one of 90 GOP House members to oppose the deal.
Both said they voted no because of how the CR affects the military. The vote was particularly difficult for Thornberry, a Texan and one of just four to vote against a deal that included hurricane aid.
McCain released a statement Tuesday echoing the concerns raised in Mattis' letter: "Congress's vote to begin the year on yet another continuing resolution is inexcusable. It says that we are willing to accept the status quo for our military—where more service members are dying in training than on the battlefield. We must not repeat this mistake in December."
While the military's biggest issue comes if there's a continuing resolution for the entire fiscal year, Mattis warned that even a three-month stopgap measure has detrimental effects.
"Impacts begin immediately, within the first 30 days of a CR. By 90 days, the lost training is irrecoverable due to subsequent scheduled training events," Mattis wrote.
Under a 90-day CR, Mattis wrote, ship maintenance for 11 Navy ships will have to be delayed, noting that "the shipyards' capacity is not capable of 'catching up' lost work." The Pentagon chief said hiring and recruiting would be curtailed under a CR, and defense contractors would be unable to begin 18 new programs for the Army.
A six-month CR — which is a possibility unless Congress can strike a budget deal — would also impact 24 more Army programs, seven Navy contracts and six Air Force programs.
Mattis also made a pitch for Congress to lift the Budget Control Act spending caps, which were passed in 2011 as part of another deal to lift the debt ceiling and place a limit on Pentagon spending.
The Trump administration's proposed budget is more than $50 billion above the caps, which means unless Congress raises the spending limits, the defense increase will not materialize.
"In the long term, it is the budget caps mandated in the Budget Control Act that impose the greater threat to the Department and to national security," Mattis wrote. "BCA-level funding reverses the gains we have made in readiness, and undermines our efforts to increase lethality and grow the force."