Ayu is accused of giving $11,682 to Timi Frank and Paul Ofana to hire the Movement for the Emancipation of the Niger Delta (MEND) to cause insurrection in the delta, Africa's oil heartland, newspapers reported on Saturday.
The three are facing five charges of terrorism.
The charges, which carry a death sentence, were committed in early February. No date has been set for a court hearing, Nigerian newspapers said.
"Ayu provided the sum of one million, five hundred thousand naira to Frank and Ofana to recruit, mobilise and sponsor armed persons"
"Ayu ... provided the sum of one million, five hundred thousand naira [Nigerian currency] to Frank and Ofana ... to recruit, mobilise and sponsor armed persons for the purpose of causing insurrection and carrying out acts of terrorism in the Niger Delta," the Vanguard newspaper reports quoting the charges.
A spokesman said on February 2 that the government had uncovered a plot by Abubakar to destabilise Nigeria, days after the vice-president was reported as saying Abuja had approved $2bn for arms to quell the worsening insecurity in the delta region.
MEND, a faceless group which emerged in late 2005, says it is fighting for the people of the impoverished delta to gain control of oil revenues.
It has also made political demands.