Former Prime Minister Yingluck Shinawatra said the junta had fined her 35.7 billion baht over the rice pledging scheme.
She said outside a Bangkok court on Friday that she had received a notice two days ago ordering her assets to be seized.
"Such an order has violated my rights and is not fair," she said as supporters greeted her outside the Bangkok courthouse.
"I affirm that I will exercise all my rights to deny this allegation and the civil charges," she said.
The order, signed by Deputy Finance Minister Wisudhi Srisuphan and permanent secretary Somchai Sujjapongse on Oct 13, and received by Yingluck on Wednesday, details allegations and losses to the government which occurred from the scheme.
It demands Yingluck pay the money to the ministry within 30 days, and allows her the right to appeal within 90 days if she does not agree with the order.
The ex-premier added that she would not comment further as the country is still grieving the death last week of its revered monarch Bhumibol Adulyadej.
But she has previously called on the junta to file civil claims in court instead of ordering the 35.7-billion-baht fine, 66 times the 579-million-baht assets she declared in June 2015.
Gen Prayut Chan-o-cha, in his capacity as the junta chief, in mid-September issued an order by his absolute power under Section 44 of the 2014 interim constitution to have the Legal Execution Department seize the assets of state officials liable to pay civil damages under the scheme. The executors will have immunity in doing their duties.
Before the order, the Finance Ministry and Commerce Ministry were supposed to seize assets by themselves, a time-consuming process since, unlike the Legal Execution Department, they are not experts on the issue.
Ms Yingluck was charged with criminal negligence over the rice subsidy scheme and is now fighting the charges in court. Her lawyers had earlier asked the junta to put off imposing the fine until the court rules.
In addition to cases against Yingluck and senior members of her former cabinet, the junta is investigating some 850 cases related to the rice scheme for graft, government spokesman General Sansern Kaewkamnerd told Reuters.
Many of the cases involve lower-ranking public officials and members of the private sector, he said.
The scheme, which was launched in October 2011 as part of a Pheu Thai party election promise, allegedly resulted in 554 billion in losses for the country. Critics say farmers were paid overly high rates for their rice. Ms Yingluck said in her defence it was "a public policy, which aimed to help farmers".
Shortly after the 2014 coup, she was retroactively impeached and, as a result, she was banned from politics for five years.