At the time of the payments, Soco was operating in Virunga National Park in eastern Democratic Republic of Congo.
The company strongly rejects any suggestion that the payments were connected with the alleged abuse.
Last year, Soco ended its activities in Virunga, which is home to some of the last remaining mountain gorillas.
The BBC's DR Congo reporter Maud Jullien says the months the company spent exploring for oil in the park, a Unesco World Heritage site, angered campaigners and sparked international outrage.
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The 7,800 sq km (3,000 sq miles) park is one of the most ecologically diverse places on Earth, but it has suffered from the years of lawlessness and conflict between armed groups based in eastern DR Congo attracted by the area's rich mineral resources.
Soco used Congolese government soldiers to secure its staff and infrastructure in the volatile region.
Cheques and receipts obtained by the campaign group Global Witness, and seen by the BBC, show the company paid an army major called Burimba Feruzi.
The payments total $42,250 (Â£27,290) over the course of two weeks in spring 2014.
That is the equivalent to several years' salary for a Congolese army major.
Several people have said they were threatened by Maj Feruzi.
One person said that men following the major's orders had tortured him, stating it was because he had opposed oil exploration.
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The London-listed company said it has never denied funding the work of the Congolese army "or that Maj Feruzi was the DRC army's military liaison officer assigned to Soco's security".
"However, we strongly refute any suggestion that this funding was in any way improper or connected with alleged acts of intimidation or violence," it said in a statement.
It said it was not allowed to enter the area where it carried out exploratory tests without a military escort.
"The soldiers assigned to Soco's security escort were always under the full command and control of the DRC army," it said.
The BBC has seen evidence that British firm Soco made payments to a Congolese army major accused of using violence to intimidate oil exploration opponents.