More than 70,000 Syrians are trapped in "hellish conditions" in a remote, arid strip of no-man's land on the Syrian side of the border, the rights group said.
Jordan closed the border, halting aid deliveries to a makeshift camp, after a bombing claimed by the Islamic State group killed seven Jordanian soldiers in June.
Since then the kingdom has only allowed a single delivery of aid to the refugees, in August.
But it said yesterday it would allow further deliveries by crane across the border in the coming weeks.
"News that humanitarian assistance will be resumed to tens of thousands of refugees... Comes as a welcome relief," said Audrey Gaughran, Amnesty's director of global issues and research.
"However, we are worried by reports that aid will be lobbed across the border by crane or that refugees will be coerced... To move to areas where they may be at risk of attack in order to receive it."
She called for unfettered humanitarian access and for the refugees to be allowed onto Jordanian territory.
Jordanian officials said the bomber had come from a camp just across the border.
Jordan says it is hosting over 1.4 million Syrians on its territory, of which 630,000 are registered with the United Nations.
The kingdom has repeatedly said it is not receiving enough international help to share the burden.
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