The advice was given just as the Action Congress of Nigeria urged the Police Service Commission to address the causes of the fracas in the House rather than the symptoms in its investigation of the role of the police in the crisis.
The comments by the Presidency and the ACN followed a July 9 petition by Amaechi to Jonathan on the free for all that led to infliction of injuries on some lawmakers following an attempt to impeach the Speaker of the House, Mr. Daniel Amachree by a group led by Mr. Evans Bipi.
Amaechi had in the petition which was also addressed to the PSC Chairman, Mike Okiro, requested the immediate transfer of the Commissioner in charge of the state Police Command, Joseph Mbu.
He also sent copies of the petition in which he detailed Mbu's alleged atrocities to Senate President David Mark and the Speaker of the House of Representatives, Aminu Tambuwal.
But the Presidency through the Special Adviser to the President on Political Matters, Ahmed Gulak, wondered why the governor's priority should be on the redeployment of the police commissioner at a time when efforts were ongoing to fly an injured lawmaker, Michael Chinda, abroad for treatment.
Gulak, in an interview with one of our correspondents in Abuja on Saturday, however gave an assurance that the President would look at the merits and demerits of Amaechi's petition before taking a decision.
Insisting that the governor should be held responsible for the fracas, the Presidential aide reminded Amaechi that the immunity from prosecution which he currently enjoys as a governor would end on expiration of his tenure.
He therefore asked security agencies to investigate the fracas thoroughly and keep the file.
Gulak said, , "It is true that as a sitting governor, he enjoys immunity but immunity cannot be forever.
"Security agencies should investigate the matter (fracas) thoroughly and keep the file because I still find it amazing and tragic for the governor to go into the House of Assembly to play active role in the fracas. It amazes me.
"But one thing is sure, the President will read through his (Amaechi's) petition. He will study it and look at its merits and demerits. It is after that that the President will direct relevant authorities appropriately on the matter.
"The governor had a game plan from the beginning. He wants the commissioner of police redeployed. He is not talking about a member of the House of Assembly who is the Majority Leader and his (Amaechi) security details beat to a coma.
"The lawmaker has been in a coma since that incident on Tuesday and will be flown abroad for treatment. The governor is not talking about that one, his major preoccupation is the redeployment of the police commissioner."
But the Rivers State Government and the ACN, said Amaechi's quick intervention prevented the free-for-all in the House of Assembly from escalating.
The Chief of Staff, Rivers State Government House, Port Harcourt, Mr. Tony Okocha, argued that Gulak should have called for an inquiry into how thugs gained entrance into the House.
"It is most unreasonable to contemplate. Rather conversely, Amaechi ought to be commended for his brave intervention and rescue mission even at the risk of his life. Gulak should be suggesting an inquiry into how armed thugs got into the Assembly and at whose behest," he said in an SMS message to The PUNCH.
"He (Gulak) should be able to absolve the Presidency from complicity knowing the relationship between Bipi and the Presidency. Nigerians are better aware than he thinks," Okocha added.
The Police headquarters has however summoned the orderly to Amaechi, who was captured in a video engaging in a brawl with a lawmaker during the fracas in the House.
"It is true that the police orderly who played a prominent role in the fracas has been summoned by the IG. He was captured in the video engaging in a fight with a lawmaker contrary to Force discipline and code of conduct for officers," a source close to Louis Edet headquarters of the force said on Sunday.
Inspector-General of Police, Mohammed Abubakar, had set up a panel headed by the Deputy Inspector-General of Police in-charge of Operations, Philemon Leha, to probe the impasse.
When contacted on Sunday, the Deputy Force Public Relations Officer, Frank Mba, said investigation into the crisis was ongoing and that the force would not hesitate to invite anyone involved in the incident.
"You are aware that the investigation panel set up by the IG has begun its work; so anyone found to have participated in the fracas can be invited . Everyone that played a role in the incident will be summoned," he said.
The ACN, in a statement on Sunday by its National Publicity Secretary, Alhaji Lai Mohammed, said a statement credited to PSC Chairman, Mike Okiro, suggested that the commission was only interested in the role of the police in the fracas.
It stated that the commission was not interested in how the police hierarchy in the state wantonly allowed the flare-up because it was acting to protect certain interests at the expense of the public.
The statement reads in part, "Governor Amaechi has documented, in a much-publicised letter to Mr. Okiro, how the Police Commissioner in Rivers, Mr. Mbu has thrown professionalism to the winds in pursuing his narrow agenda at the expense of the security of the state.
"It is on record that this 'political policeman' has worsened the security situation in the state since he assumed office in February 2013 by undermining the authority of the Governor as the Chief Security Officer of his state; undermining the security structure put in place by the State Security Council and compromising the council to such an extent that members no longer speak their minds freely during meetings.
"These are the issues we expect a non-partisan PSC to address with a view to sanctioning whoever it is that paved the way for the disgraceful show that was put up under the klieg light last week. While the PSC will be right to sanction even the policemen shown to have acted badly that day, the sanctions must extend to their bosses who allowed that to happen."
ACN also insisted that Jonathan, his aides and the Peoples Democratic Party could not distance themselves themselves from the Rivers crisis.
It said, "Anyone with a conscience knows that the root of the problem in Rivers lies in the President's bedroom, and no amount of fanciful statements or name calling targeted at those who are conscientious enough to call a spade a spade will change that.
"This is why we are insisting that the President must be impeached by the National Assembly for his failure to respect the rule of law and the constitution of the Federal Republic of Nigeria which he has taken an oath to uphold."