Beefed up security checks at the Texas border are snarling the supply chain — and could even contribute to an avocado and tomato shortage in the US, according to a new report.

The issues are related to a border security directive issued by Gov. Greg Abbott last week, ordering Texas Department of Public Safety troopers to perform secondary inspections on vehicles entering the country at the Texas-Mexico border, even after a first inspection at the port of entry, according to the Texas Tribune.

Commercial trucks carrying imported goods are being inspected at select ports of entry across the Texas border, delaying delivery by hours.

“This continues to add disruption to our supply chain. It’s just something we don’t need right now,” Ermilo Richer, owner of a shipping and import company in Laredo, told the Texas Tribune.

Abbott launched the new security measures Wednesday ahead of the Biden administration’s expected lift to the pandemic-era Title 42, an emergency order which allowed the feds to turn away migrants at the border.

The Texas International Produce Association wrote a letter to the governor, “imploring him” to stop or change the secondary inspections due to the supply chain snafus.

“Warehouses have staff sitting idle, with no trucks to unload. Buyers in other parts of the country cannot understand why their product is not available,” reads the letter.

“US trucking companies are losing money as they sit around for days with no loads to haul. I have even heard from a member that a trucking company is refusing to send trucks south of San Antonio out of concern there will be no cargo available. This is destroying our business and the reputation of Texas. I foresee companies making plans to move their business to New Mexico and Arizona,” the letter says.

Abbott made the case Wednesday that secondary inspections of commercial vehicles are needed because they are often used to smuggle drugs or people.

But Rep. Henry Cuellar (D-Laredo) said Texas troopers aren’t allowed to inspect cargo and can only perform mechanical inspections.

“I don’t know what the rationale is. If you’re worried about too many people coming in but you can’t inspect the cargo, that doesn’t accomplish anything except make things uncomfortable and have a negative impact on commerce,” Cuellar told the Texas Tribune.

Troopers plan to inspect every vehicle and each inspection could take about 45 minutes, Cuellar told the outlet.

Abbott, who is currently running for re-election, did not respond to The Post’s request for comment on how his border initiative may be impacting the economy.

His opponent, El Paso Democrat Beto O’Rourke, wasted no time in pouncing, tweeting that Abbott’s “newest political stunts” are making inflation worse.

“I just spoke to a small business owner in McAllen who imports produce from Mexico. Her broker said that of the 250 produce trucks that he typically helps to cross each day at the Pharr port of entry, only 68 could get through on Friday. The rest were stuck,” tweeted O’Rourke.

The Democratic gubernatorial candidate says the McAllen produce importer told him Monday would be chaos since their warehouses will be empty, and trucks showing up to take those fruits and vegetables to Texas and other parts of the country will have nothing to load.

Mexico is Texas’ number one trading partner, doing $442 billion in business.

Cuellar told the Texas Tribune if this continues, there could be shortages of avocados, tomatoes and other Mexican goods that are popular in the US.