Speaking in parliament, Mr Kiir defied calls from the UN and African Union to pull out troops, after three days of clashes with Khartoum.
Meanwhile, Sudanese aircraft are reported to have attacked a regional capital in the South.
The fighting is the worst since South Sudan gained independence last July.
In response, Sudan ordered a general military mobilisation and has vowed to act with "all means" against the attack. It has also pulled out of African Union-led negotiations with South Sudan.
Mr Kiir said he did not want war with Khartoum, but said his country had to act in self-defence.
"I always say we will not take the people of South Sudan back to war, but if we are being aggressed (attacked) like this we will have to defend ourselves," he said.