Uefa confirmed on Tuesday that 23 clubs have not been paid prize money, pending further investigation, for breaching Financial Fair Play rules.
But the La Liga pair have come out fighting, issuing press releases saying they are fully behind the initial decision and will remain 'transparent' throughout.
A statement on Malaga's official website read: “Further to the previous statement made by the club, a complete internal restructuring process got underway over a month ago, aiming to guarantee the future viability of the club.
"The starting point of this process was to address the financial commitments, and find a balance between income and expenditure, in order to meet with the Uefa fair play requirements.
“The club is still fully immersed in this process, and has now stabilised the financial situation with other clubs, employees and players, and is in negotiations with ‘Hacienda’.
"Although a definitive agreement has not as yet been reached, the amount owed by the club has been significantly reduced over the last month. Malaga Club de Futbol has informed Uefa of this situation, and there is a transparent relationship between both organisations.
“The inclusion of Malaga Club de Futbol in the list published today by Uefa is a precautionary measure and not a penalty, which can be lifted as soon as an agreement is reached with the "Agencia Tributaria," something which the club has been working towards for several weeks.”
Atleti were also swift in their response and released the following statement:
"On May 10, 2012, Club Atletico de Madrid SAD obtained from the Committee of First Instance of the RFEF [Spanish Football Federation] the right to participate in Uefa competitions. Subsequently, Uefa announced our admission on June 15, that the club could participate in the Uefa Europa League 2012/13.
"Therefore, Club Atletico de Madrid S.A.D. fulfilled in the first instance with every one of the requirements of regulation and licensing Uefa Financial Fair Play to participate in European competitions.
"This regulation establishes a monitoring procedure or permanent financial control for those clubs who have been licensed with Uefa, which implies the obligation to submit, on a quarterly basis, certain financial information that reliably demonstrates compliance with the monitoring requirements imposed by the panel of financial control.
"In the quarterly monitoring of June, Club Atletico de Madrid SAD submitted all documentation required by Uefa agencies.
"However, we would like to clarify that the measure notified today by Uefa assumes no seizure of any amount to Club Atletico de Madrid SAD, but it is an injunction issued in Uefa licensing regulation until the adoption of a control panel final decision, which we believe will be favourable.”