Republican Dana Rohrabacher's office said he was a "last-minute" addition to the delegation when one of the members cancelled days before travelling. He was prevented from travelling on Friday.
Rohrabacher, chairman of the House Foreign Affairs Subcommittee on Oversight and Investigations, has been a vocal critic of the "corrupt Karzai government and the US failed strategy of foisting a western-style democracy from a central government in Kabul," his communications director Tara Setmayer told AFP.
Last month, he called for a US probe into whether Karzai is misappropriating foreign aid funding to benefit himself and his family, at a time when Congress was considering President Barack Obama's 2013 budget proposal that includes $2.5 billion for Afghanistan.
"When Karzai found out Dana was a part of the CODEL (congressional delegation), he told the State Department the entire CODEL would be denied if Rohrabacher was included," Setmayer said.
"So, Secretary (Hillary) Clinton personally relayed Karzai's message and personally petitioned Dana not to continue on with the delegation. Out of respect, he obliged and stayed behind in Dubai."
The delegation continued on without him, and Setmayer said the lawmakers met Sunday with former leaders of the Northern Alliance, which cooperated with the United States to oust the Taliban from power after the September 11, 2001 attacks.
Texas Republican Louie Gohmert was part of the delegation that was in Afghanistan over the weekend, and his staff confirmed they met with several opposition figures.
They included Abdullah Abdullah, who ran against Karzai in the contested 2009 election and is now Afghanistan's main democratic opposition leader, and Ahmad Zia Massoud, a founder of the Afghan National Front and brother to Ahmad Shah Massoud, the iconic anti-Taliban commander who was killed by an Al-Qaeda bomb two days before 9/11.
The lawmakers also met with Abdul Rashid Dostum, a long time ethnic Uzbek warlord who in 2010 was named Karzai's army chief of staff and is now an Afghan National Front leader and chairman of his political party, the National Islamic Movement.
The delegation dispute comes amid lingering tensions between Washington and Kabul.
The 130,000-strong US-led NATO forces helping the Afghan government fight a decade-long Taliban insurgency is due to end combat operations and pull out by the end of 2014 and the two countries are in talks about their future relations.
Officials on both sides have expressed hope that a strategic partnership agreement governing post-2014 ties could be signed ahead of a NATO summit in Chicago next month.
Negotiations have been further complicated by a US soldier's murderous rampage that left 17 Afghan villagers dead. Staff Sergeant Robert Bales has since been flown out of the country back to the United States.
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