Eritrea has denied reports that it delivered weapons in the last few days to Somali Islamist group al-Shabab.
The Kenyan army said two planes landed in Baidoa with weapons and ammunition for al-Shabab. It did not specify where the aircraft had come from.
A UN report earlier this year accused Eritrea of supporting al-Shabab.
Kenya sent troops into Somalia in mid-October as it blames the Islamist group for a spate of kidnappings - allegations al-Shabab dismisses.
The al-Qaeda-linked group controls much of central and southern Somalia.
Meanwhile there are conflicting accounts of losses following a battle involving Kenya, Somali government forces and al-Shabab on Tuesday on the road from the border town of Liboi to Kenyan forward troop positions inside Somalia.
The BBC's East Africa correspondent Will Ross says it is increasingly hard to know who is telling the truth in what is a hard-fought propaganda war.
An al-Shabab spokesman said seven Kenyan soldiers were killed and two armoured vehicles destroyed during the ambush - which Kenya denies.
Somalia's internationally recognised transitional government said its forces, backed by Kenyans, had killed 36 insurgents in the counter-attack.
Kenyan army spokesman, Maj Emmanuel Chirchir, said two planes of arms had landed this week in the central town of Baidoa with the weapons for al-Shabab.
The BBC has not been able to independently verify whether any arms have landed in Baidoa. Media reports in Kenya and Somalia had suggested they came from Eritrea.
"The government of Eritrea states categorically that these accusations are pure fabrications and outright lies as Eritrea has not sent any arms to Somalia," Reuters news agency quotes Eritrea's foreign ministry as saying in a rare statement.
Maj Chirchir warned that air strikes against al-Shabab targets were imminent to prevent the weapons reaching militant bases.
He advised civilians in 10 towns to stay away from al-Shabab camps.
His warning follows controversy over the aerial bombardment of Jilib on Sunday in which he says a Kenya fighter jet hit al-Shabab positions, killing 10 militia fighters.
But the medical charity MSF-Holland said at least five people, including three children, died after a camp for internally displaced people was bombed.
Our correspondent says there is a real danger that a reliance on air power will make civilians more vulnerable and lead to the Kenyan mission becoming unpopular in Somalia.
People abducted from Kenya since September include a French woman suffering from cancer, who French authorities say has since died; a British woman taken from a coastal resort, whose husband was killed in the raid; and a Kenyan driver and two Spanish aid workers seized from the Dadaab refugee camp near the Kenya-Somalia border.
After two decades of civil conflict, Somalia is awash with guns and analysts say any number of groups could have carried out the kidnappings - including pirate gangs.
Al-Shabab is locked in a battle with the weak UN-backed interim government for control of the parts of the country which are currently outside its power, particularly the capital, Mogadishu.