The US Consulate General in Edinburgh has defended using Prestwick Airport for US planes carrying weapons to refuel before flying to Israel.
The US Consulate General defended the use of Prestwick
Cecile Shea met Green MSPs at Holyrood on Tuesday, where she described the UK as the "most important ally" of the US.
Ms Shea did however echo George Bush's apology for making military flight stopovers without prior warning.
However, Green MSP Patrick Harvie said many Scots were angry at one side being armed in "a brutal conflict".
The BBC has learned that US military flights carrying bombs to Israel will no longer use civilian airports in the UK, and only military airfields will now be used during the Lebanon conflict.
A protest was staged at Prestwick Airport on Sunday, where several controversial flights are known to have landed, believed to be carrying bombs to Israel.
Speaking after holding talks with Green MSPs, Ms Shea said US officials in London and Washington were aware of their discussions.
"Britain is our closest and most important ally, and they will be interested in what various members of the Scottish Parliament have to say," she said.
She echoed President Bush's apology for using Prestwick without completing the necessary paperwork.
"I reiterated the President's apology, with a couple of flights last weekend we didn't do some of the early-warning paperwork that we might usually have done," Ms Shea said.
Ms Shea said US Secretary of State Condoleezza Rice was working towards a durable ceasefire and was attempting to agree on a multi-national task force to go into southern Lebanon.
About 150 people took part in a demonstration on Sunday
But she added: "Honestly, I don't think the flights are the issue for most people, it's finding a way to a ceasefire, to a long-term solution to the problem."
The US Consulate General defended the sale of weapons to Israel and said the root cause of the conflict was Hezbollah firing rockets at civilian areas of Israel.
Pressed on Green concerns about so-called rendition flights, she said the US remained committed to human rights and that it did not extradite people to countries where they were tortured.
Mr Harvie described the meeting as "a frank exchange of views" and said the issue was not about the paperwork for flights.
"This is about arming one side in a brutal conflict in the knowledge civilian lives will be destroyed," he added.
"It seems astonishing the governments including the UK and the US are still not willing to call for an immediate ceasefire.
"I tried to convey to the consul that many, many people in Scotland are reacting with great anger at not only the US foreign policy but the way that the US seems to take for granted it can use UK and even Scottish airports."
The meeting with the consul was arranged after the Scottish Greens contacted the US ambassador in a visit to the parliament in March
The Irish Government has refused to allow its airports to be used as a stopover for munitions.