A judge at the Federal High Court in Lagos on Tuesday ordered the apartments to be forfeited to the Economic and Financial Crimes Commission until the probe was concluded.
Alison-Madueke, who served under former president Goodluck Jonathan until 2015, is at the centre of money laundering and bribery enquiries in several countries.
She was arrested in London in October 2015 as part of a British investigation into international corruption, and remains on bail.
The 57-year-old Alison-Madueke is one of the highest-profile figures from the former administration being targeted as part of President Muhammadu Buhari's anti-corruption drive.
Judge Mojisola Olatoregun was told the properties in question were in the Banana Island gated community and Admiralty Estate area of the city.
They had a combined value of $4.76 million. The EFCC investigation is seeking to determine whether they were bought with the proceeds of crime.
Alison-Madueke has previously had several homes and apartments seized by court orders.
In October, she lost properties in Lagos, Abuja and Port Harcourt valued at 2.6 billion naira ($7.2 million).
They were bought through front companies linked to her and her cousin, Donald Chidi Amamgbo.
He has told the EFCC the companies had been registered to hold property on behalf of Alison-Madueke, who was the first female president of OPEC.
In August, a judge ordered the confiscation of Alison-Madueke's $37 million luxury apartment complex on Banana Island.
In the latest case, Amamgbo is listed as a respondent with Alison-Madeueke and two companies said to own the luxury penthouses. Amamgbo owned one of the firms.
The court was told payments to buy the flats were made by Angela Jide-Jones and Atlantic Drilling Concept Limited.
Jide-Jones' husband is Jide Omokore, a close associate of Alison-Madueke, who is facing investigations and asset seizures in Nigeria and the United States.
Atlantic Energy Drilling Concept Limited is his company.
In September, a court in south London ordered a freeze on five upmarket properties in the British capital linked to Alison-Madueke.
The former minister is listed as a defendant alongside Omokore, Kolawole Aluko, Amamgbo and another oil billionaire, Benedict Peters.
The properties were held in the name of three companies, listed as third parties.