The statement described the congressional action as "a joint resolution that purports to direct the President to remove United States Armed Forces from hostilities in or affecting the Republic of Yemen, with certain exceptions".
In a statement to the Senate on Tuesday, the Commander-in-chief called the resolution "an unnecessary, unsafe attempt to weaken his constitutional authorities".
He also claimed that USA support was needed to "protect the safety of the more than 80,000 Americans who reside in certain coalition countries that have been subject to Houthi attacks from Yemen", referring to the Iran-aligned forces in the country.
"Congressional engagement in those endeavors would be far more productive than expending time and effort trying to enact this unnecessary and unsafe resolution that interferes with our foreign policy with respect to Yemen", he said.
Many legislators also criticised the president for not condemning Saudi Arabia for the killing of a Saudi journalist Jamal Khashoggi, who had been critical of the kingdom. Members of Congress have expressed concern about the thousands of civilians killed in coalition airstrikes since the conflict began in 2014. The conflict has killed tens of thousands of people, fueled a major cholera outbreak and driven the Arab world's poorest country to the brink of starvation.
No one was surprised by the veto - had Trump wanted to comply with the resolution, he could have withdrawn support to Saudi Arabia at any time. Mr Trump called the conflict in Yemen "a "cheap" and affordable way for Iran to cause trouble for the United States and for our ally, Saudi Arabia".
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The resolution passed 54-46 last month, with Republican Sens.
House Speaker Nancy Pelosi denounced Trump's veto, saying it would serve to "perpetuate America's shameful involvement in this heartbreaking crisis".
The president said USA forces are not engaged in hostilities "in or affecting Yemen" apart from counterterrorism operations against al Qaeda in the Arabian peninsula and the Islamic State.
Kaine accused Trump of turning a blind eye to Khashoggi's killing and the jailing of women's rights activists in Saudi Arabia.
Before Trump signed his second veto, Democratic California Rep. Ro Khanna told The Daily Caller News Foundation he hoped the president would stand against endless wars and sign the resolution.
The bill passed the House 247-175. "It sets back the hopes for respite for the Yemeni people, and leaves the USA upholding a failed strategy". Trump had declared a national emergency so he could use more money to construct a border wall.