The New York-based group Human Rights Watch on Monday said Saudi border guards had fired "like rain" on Ethiopians trying to reach Saudi Arabia from Yemen.
HRW accused the Saudi guards of using explosive weapons as part of attacks that appeared to be "widespread and systematic," and said the killings may amount to crimes against humanity.
The report sparked global outrage after its publication, although a Saudi government source quickly dismissed the allegations as "unfounded and not based on reliable sources."
In a new statement on Thursday, a Saudi government source "denounced the raising of false allegations by some organizations about the Kingdom and the publication and promotion of politicized and misleading reports in the context of malicious media campaigns that are repeatedly raised for suspicious goals and objectives," the official Saudi Press Agency reported.
The source, whom SPA did not name, said Saudi authorities were committed to upholding human rights principles and had previously provided medical care to "groups of people who were subjected to gunshot wounds by armed groups to push them to enter the Kingdom by force."
In 2015, Saudi Arabia mobilized a military coalition in an effort to stop the advance of Iran-backed Huthis in Yemen, who had seized the capital Sanaa from the internationally recognized government the previous year.
In its report, HRW referred to testimony from migrants who said Houthi forces worked with people smugglers and would "extort" them or keep them in detention centers where they were "abused" until they could pay an "exit fee" and head to the border.
In response to a letter from HRW, Houthi authorities denied working with people smugglers, describing them as "criminals."
The United States on Monday called on Saudi Arabia "to undertake a thorough and transparent investigation" into the alleged killings by Saudi border guards.
On Tuesday, Ethiopia said it would launch an investigation "in tandem" with Saudi authorities.
But Thursday's statement out of Riyadh made no mention of an investigation.