NAIROBI, Kenya, April 10— Ugandan security forces arrested about 1,000 civilians in Kampala today, wounding some of them, witnesses in the Ugandan capital said. It was the third mass detention in a month in what the authorities called a drive against anti-Government guerrillas.

Ugandan sources reached by telephone from Nairobi reported shooting this morning in the suburb of Bwaise near Mulago Hospital. A few hours later, trucks carrying about 1,000 civilians, many of them bleeding and apparently beaten, were seen heading along the road to Entebbe, they said.

In mid-March, the Ugandan authorities detained thousands of civilians -most of them men between the ages of 15 and 35. The arrests followed a mortar attack on Feb. 23 against Kampala's Malire barracks. The Government reported 67 guerrillas and 5 soldiers were killed in the attack.

Last Wednesday, the security forces seized thousands of other civilians -again, mostly young men. Many of the detainees have been released, but relatives of hundreds of others say they have not heard from them since their arrest.