Madut Bior, GoSS acting minister for Information, said the government was saddened by the incident.
He added that the authorities are making efforts to bring the culprits to book.
Mr. Madut said the act was part of attempts made by the anti-peace and anti-referendum camps to discredit south Sudan as a lawless region.
GoSS minister for Internal Affairs, Gier Chuang, said there is no deliberate plan by the government of south Sudan to mistreat foreigners in the region.
Five people including two Ugandans were killed and six others seriously injured after an unknown gunman opened fire at Customs market, in Juba on Friday 1 October.
GoSS President Salva Kiir Mayardit expressed condolences to the families, friends and relatives of the bereaved, according to a carefully worded message delivered by Minister Chuang on Monday.