Opposition lawmaker Isaac Adongo compared Vice-President Mahamadu Bawumia's economic management of the embattled West African nation to Maguire's performance on the pitch.
In an address shared widely on social media last year, Adongo compared Bawumia to Maguire, who he described as "the biggest threat at the centre of the Manchester United defence".
The reference was part of a wider speech accusing Bawumia of mismanaging the economy and inflicting hardship on citizens.
Ghana is grappling with its worst economic crisis in a generation brought on by spiralling public debt, which has triggered rampant inflation and weakened the local currency.
In a similar debate on the 2024 budget on Tuesday, Adongo said Maguire had "turned the corner" and took back his analogy.
"I now apologise to Harry Maguire," Adongo said. "He is a transformational footballer... now scoring goals for Manchester United."
Maguire accepted the apology in a post on X on Wednesday.
"See you at Old Trafford soon," he wrote, referring to the home of Manchester United.
But he did not relent his criticism of Bawumia, accusing him of "roaming" around the International Monetary Fund (IMF) "with a cup in hand".
Ghana's government turned to the IMF for help last year. The Fund approved a three-year, $3 billion programme in May, with an immediate disbursement of $600million.
Bawumia heads the government's economic management team as has been selected as the ruling party candidate for 2024 elections.