WASHINGTON — With the fiscal year set to expire at the end of September, Secretary of Defense Jim Mattis is warning that a stopgap funding measure would have a serious impact on a Pentagon attempting to modernize its capabilities.

Operating under a continuing resolution, or CR, would be “about as unwise as can be,” Mattis told reporters this week at the Pentagon.

It is a tradition that all those serving as secretary of defense have grown used to over the past five years: sounding the alarm about what a CR will do to readiness and modernization, publicly begging Congress to fix the problem and then getting on with life when the budget is inevitably passed toward the end of the year.

There are indications that Congress will follow that pattern this year, with the expectation of a CR to keep things working after September before a final budget is arranged around Christmas. But until that situation sorts itself out, Mattis will most likely follow the script laid out by Ash Carter, Chuck Hagel and Leon Panetta — sounding the alarm about the impact of a CR, which freezes funding at levels from the previous year while preventing new start programs from launching.

“We cannot start new programs, so where you’re trying to adjust to the changing character of warfare — electronic warfare, space issues, cyber issues, counter-UAS efforts … we cannot start those new programs,” Mattis said of a CR. “It just creates unpredictability. It makes us rigid. We cannot deal with new and revealing threats. We know our enemies are not standing still.”

Industry is also keeping a wary eye on the budget situation, with two major trade groups telling their members this week to start making contingency plans in case a government shutdown occurs.  Mattis acknowledged the impact on industry, noting that a CR forces those companies to hit pause on investing in new projects.

“American industry says, ‘Whoa, you know, I can start doing something here.’ And then there’s no budget for it down the road, so I’ve just put a lot of money into my capital investment, and now, it’s going to sit and idle,” he said of industry response.

The secretary said he would work closely with the defense committees to “try and avoid the damage” that would result from a CR, although he was careful to say, “I wouldn’t call it lobbying.”

Asked how confident he was that Congress would handle the budget, Mattis demurred, saying, “I save those kinds of feelings for others. I just do the job.”