Earlier this month Mutharika gave prosecutions director Ishmael Wadi 24 hours notice after he dropped corruption charges against Malawi's former president, Bakili Maluzi.
Mutharika, who came to power on a "zero corruption" ticket, nominated Tumaliske Ndovi, Commissioner of Police and head of the police service prosecutions department, as Wadi's successor, but his confirmation of office by Parliament's Public Appointments and Declaration of Assets Committee was rejected because it wanted an explanation as to why Wadi was fired.
Analysts said the impasse was an indication of the poor relationship between the presidency and parliament, and this spat could have serious implications for the country.
"The public appointments committee is justified to ask for an explanation from the president. If you look at the issue of Mr Wadi, he was fired, technically, although he resigned later on. Why should the committee be interviewing people anyway?" said Happy Kayuni, a political science lecturer at Chancellor College.
"Legally, the president is not mandated to give reasons to the committee for firing people he hires. Likewise, it will not be a good reason for the committee to say that they are not confirming someone because the president is not giving reasons why he fires people," he said. "If the committee does not want individuals in such positions, what they could say is that the person they want to confirm is not qualified."
The president's 'resign or be fired' ultimatum came after Wadi did not inform him that he was dropping the 42 charges of corruption, fraud and abuse of office brought against Maluzi in July this year. Wadi reportedly said he dropped the corruption case against Maluzi after Mutharika suspended the main investigator in the case, Gustav Kaliwo.
During Muluzi's term of office the committee rarely rejected appointments because his United Democratic Front (UDF) party held a majority in parliament, which Mutharika does not.
Muluzi stepped down from office in 2004 after a decade in power and chose Mutharika to run for president, but Mutharika resigned from the UDF after eight months in power, citing hostility from the party over his anti-corruption drive, and formed the Democratic Progressive Party (DPP) in February last year.
DPP secretary-general Heatherwick Ntaba hinted that the new public prosecutor could resurrect the Muluzi case once he was appointed, but Muluzi's legal representative, Fahad Assani, and the UDF's publicity secretary, Sam Mpasu, said they hoped the corruption case against the former president was now "dead and buried".
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