While fishing should in theory be held in check by the environment, with low fish stocks pushing up costs, subsidies can keep unprofitable fleets at sea.
It is widely agreed that action is needed to protect a crucial resource that millions of people depend on for their livelihoods.
In 2017, the Food and Agriculture Organization estimated that one third of global fish stocks were overfished.
Global fisheries subsidies are meanwhile estimated at between $14 billion and $54 billion a year, according to the WTO.
But two decades of negotiations have stumbled over a range of issues, and members failed to meet the latest UN deadline to reach an agreement by December 2020.
But talks have intensified in recent months.
Okonjo-Iweala, who took the reins of the global trade body in March, has made clinching the long-awaited fisheries deal by the end of this year a priority.
"Unsustainable fishing practices continue to take a toll on our oceans, encouraged by the government financial support we are seeking to discipline," she lamented earlier Thursday.
Colombian ambassador Santiago Wills, who chairs the WTO fisheries subsidies negotiations and who drafted the text being discussed, also stressed the urgency of finding a deal.
"Twenty years has been long enough. If we continue (negotiating) for another 20 years, there won't be any fish left," he told reporters.
Reaching any kind of an agreement at the WTO can meanwhile be hard, because all decisions require a consensus among all member states.
One of the main stumbling blocks in the fisheries negotiations has been a UN demand that developing countries and the poorest nations receive so-called special and differential treatment, or SDT.
While special treatment for the poorest countries is widely accepted, demands from some self-identified developing countries to be exempt from subsidy constraints has proved difficult to swallow.
Many of the major fishing nations are considered developing countries by WTO, including China, which has one of the world's biggest fishing fleets.
And there is little sign Beijing will give up that benefit.
WTO spokesman Keith Rockwell told reporters that China had told Thursday's closed meeting "they will take on obligations commensurate with their level of development".
European Commission vice president Valdis Dombrovskis meanwhile rejected the idea that all self-declared developing nations should be accorded an exception.
Instead, he said, negotiations should "provide clarity on which country and which type of fishing can benefit from flexibility".
US Trade Representative Katherine Tai also rejected the idea that "permanent" exceptions should be granted to some countries.
As for the text itself, she said it had "serious shortcomings", lamenting among other things that it does not include Washington's proposal to include a ban on forced labour on fishing vessels.