Ford said it had received reports of three cases where leaking fuel or oil ignited when trapped in a diesel particulate filter near the tailpipe of the new trucks.
In one case in Texas, a truck's hot tailpipe set off a grass fire when the driver pulled off the road, a Ford spokesman said.
The fire was quickly extinguished, and no injuries or accidents have been reported as a result of the incidents, Ford spokesman Dan Jarvis said.
"This is an important product for us and an important customer base, and we want to move swiftly to make sure this does not become a safety issue for our customers," Jarvis said.
The recall represents the second glitch since their January launch of the new Super Duty trucks.
The heavy-duty work truck is one of the automaker's most profitable vehicles and its sales success has been seen as key as Ford tries to rebound from a $12.7 billion loss last year.
Navistar International Corp. briefly halted shipments of the diesel engines for the new trucks to Ford in late February because of a contract dispute, although both sides have since been meeting under court order to resolve the matter.
Ford dealers were advised on Wednesday to stop selling the roughly 29,000 Super Duty trucks with 6.4-liter diesel engines on their lots until engine control software can be updated.
That work should begin on Thursday and could be completed in less than 10 minutes per vehicle, Ford's Jarvis said.
Super Duty trucks still awaiting shipment from the Louisville, Kentucky plant that makes them will have their engine control software updated there, he said.
Customers with the first 8,400 diesel Super Duty trucks already on the roads will be notified that they should bring their vehicles into dealerships for the same fix, said Jarvis.
Ford will send out a recall notice to customers in early April and dealers may contact them before then to alert them to the potential problem, he said.
Gasoline-powered versions of the Super Duty and previous model-year diesel trucks with 6.0-liter or 7.3-liter engines are not affected by the recall.
The software upgrade will reset the powertrain control module on the Ford trucks. In cases where the system detects unusually high temperatures in the diesel particulate filter, the control module will power down the vehicle.
The aim is to allow drivers to pull safely to the side of the road to allow it to cool before proceeding, Jarvis said.
Ford also wants to take advantage of the recall to shift a battery cable on fewer than 10,000 of the first Super Duty trucks produced in order to to keep the cable from chafing against a shield that prevents water and mud from getting into the engine.