"These allegations are unfounded and are based on untrusted sources," a Saudi official said in a statement from the official Saudi Press Agency on Thursday.
The report, which was released last week, also claimed the migrants had been trafficked by Houthi militias, who control northern Yemen.
The official condemned the allegations against Saudi Arabia as politicised and misleading.
The Saudi official said the allegations were part of a media campaign that had been launched for "suspicious goals and objectives", SPA said.
Necessary medical care was provided to groups of people who were injured by gunshots by armed groups who were trying to push them into Saudi Arabia by force, the official said.
"The kingdom is committed to the principles of human rights stipulated in its regulations, international human rights law and international humanitarian law," the official said.
Last week, Ethiopia said it is to launch a joint investigation with Saudi Arabia into the HRW report.
"The Government of Ethiopia will promptly investigate the incident in tandem with the Saudi Authorities," the Ethiopian Foreign Ministry said on X, formerly Twitter, a day after the publication of the HRW report.
The US State Department said on Thursday that the allegations by Human Rights Watch are "concerning".
"We have raised our concerns about these allegations with the Saudi government," State Department spokesman Vedant Patel said.
"We urge the Saudi authorities to undertake a thorough and transparent investigation and also to meet their obligations under international law."