Ban issued a statement saying he was concerned at the "very limited progress" made during month-long negotiations in New York, where the world's biggest arms producers have been haggling over the scope of the treaty.
Since the start, the United States has opposed the inclusion of ammunition, China does not want small arms and both Russia and China have sought restrictions on references to humanitarian law.
With talks due to end Friday on a first ever treaty to regulate the $70 billion a year industry, Ban urged the 193 UN member states to "show flexibility and work in good faith towards bridging their differences."
A draft treaty circulated Tuesday was severely criticized by rights groups, including Amnesty International and Oxfam, as full of "ambiguities and loopholes."
Syria, North Korea, Iran, Cuba and Algeria and other countries have sought from the start to thwart the treaty, diplomats and activists say.
The treaty must be agreed by a consensus of all 193 countries involved.
Even if the treaty is concluded, the conference has not yet decided how many countries must ratify it to bring it into force.
Ban "remains hopeful that the conference will yield a robust and legally binding Arms Trade Treaty," the statement released by his spokesman said.
"We owe it to all the innocent civilians who have fallen victim to armed conflict and violence," the UN chief said.
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