Saudi authorities have beheaded two Egyptians who kidnapped a nine-year-old girl and tortured her for years and executed a national convicted of murder, state news agency SPA reported.

Mohammed bin Nafe and Jamalat bin Nafe, apparently his sister, "kidnapped a nine-year-old girl from the (Muslim) Prophet's Mosque in (the holy city of) Medina, torturing and locking her up at their residence for three years and six months," the interior ministry said in a statement carried on SPA.

"Mohammed has repeatedly raped her throughout this period and the pair were planning to smuggle her out of the country," it said.

"They had also neglected the health of their children and committed violence against them, leading to the death of two of Mohammed's sons," it added.

The two Egyptians were beheaded in Medina.

In a separate statement, the ministry announced the beheading of Ali bin Mohammed al-Qahtani who shot dead a fellow Saudi, SPA reported. The man was executed in the kingdom's southeastern region of Asir.

Today's beheadings bring to 38 the number of people executed in Saudi Arabia so far this year, according to an AFP tally based on official reports.

Under the AFP count, at least 76 people were beheaded in 2011, while rights group Amnesty International put the number of executions last year at 79.

The death penalty in Saudi Arabia applies to a wide range of offences including rape, apostasy, armed robbery and drug trafficking, as well as murder, as stipulated by Islamic sharia law.