The murder happened in a region with heightened tension over land ownership.
Police said Mr Ruiz was killed as he was leaving a bank in the Bajo Aguan valley carrying the equivalent of more than $10,000 (£6,000) in workers' pay.
The Honduran authorities said he was murdered for the money, but the shooting comes a week after 11 people were killed in clashes between local land owners and farm workers.
Last Sunday, six guards were killed at a local ranch in Bajo Aguan.
Security Minister Oscar Alvarez said they were targeted by a criminal gang "dedicated to stealing fruit and de-stabilising the area".
But Deputy Security Minister Armando Calidonio blamed farm workers, who he said had tried to take over the farm.
On Monday, police found the bodies of three men and two women near the same ranch.
They are not believed to have had any links to the conflict.
A local farm workers' leader said the five had been mistaken for farm workers and killed in revenge for the killings of the guards the previous day.
On Wednesday, the government deployed 600 police and 400 soldiers to the area.
Analysts say the murder of Mr Ruiz shows the presence of the extra troops has failed to quell the violence.
The latest killing has brought the total of those who have died in clashes over the past two years to at least 36.
The Aguan Valley has some of the most productive farmland in Honduras.