Some have called it a “creeping coup”, one orchestrated by the “deep state”.

After Pakistan went to the polls in a general election yesterday, the ballot and its aftermath continues to be marred by endless and increasingly bitter allegations of malpractice and manipulation.

Violence, bombings, corruption, and above all the ubiquitous and pernicious influence of the military and intelligence services have always made elections in Pakistan fraught affairs.

Yesterday’s vote was no exception with the election getting off to the worst possible start. In thewestern city of Quettaa suicide bomber killed at least 29 people near a polling station, marking the beginning of a divisive election contest pitting cricket hero Imran Khan against the party of jailed ex-Prime Minister Nawaz Sharif.

With so much at stake and given Pakistan’s’ past election record, it would have been too much to expect this poll to be violence free.

No prime minister in the country's history has ever completed a full five-year term in office. With the polls now closed and if things continue to run smoothly, then it will only be the second time there has been a civilian-to-civilian handover of power after a full term. The first was in 2013.

But even with voting now finished many Pakistanis stillexpect an acrimonious election aftermath. True to historical form, the country’s military top brass and shadowy influential security service, the Inter-Services Intelligence Directorate (ISI), have consistently made their presence felt throughout the election campaign. Few expect that to change.

For months running up to the election, accusations have grown that the military and ISI were the hidden power behind Mr Khan’s bid to become Prime Minister.

Pakistan watchers point to themilitary’s guiding hand being visible in the partisan judiciary that went after ex-Prime Minister Nawaz Sharif who now languishes in jail with his daughter.

Sharif’s accusation, made earlier this year, that the Pakistani army facilitated the deadly 2008 terrorist attack in the Indian city of Mumbai, is widely believed to have crossed the line, one that a pliant Pakistan media dubbed as “treacherous”.

For decades Pakistan’s military leadership has regarded itself as the custodian of the nation, one still defined by its birth in the bloody partition of the Indian subcontinent in 1947.

While the military has denied it has backed any particular candidate in this latest vote, observers have warned that the security forces have helped promote candidates running for Mr Khan’s PTI party, and moved to silence its opposition.

Most analysts are convinced that the military’s favourite is Mr Khan or the “ladla", or spoilt child, as he has been dubbed by by his opponents.

The fact that almost 400,000 troops were deployed at polling stations yesterday to prevent terrorist attacks only further raised suspicions as to the army’s intentions.

“The so called soft creeping coup which was conceived by the deep state and midwifed by the judiciary during the last few years has not only culminated in full fledged authoritarian control but has also acquired some hard dimensions,” warned Afrasiab Khattak, a former Pakistan senator and political analyst in Pakistan daily newspaper The Nation before yesterday’s vote.

Others shared his concern including the Human Rights Commission of Pakistan (HRCP) who warned of “blatant, aggressive, and unabashed attempts to manipulate the outcome of the elections”.

According to independent international election observers, many were unable to gain visas until days before the vote. Typically such monitoring officials are usually in a country for weeks ahead of any polling day.

“We have never had a situation like this in any of our 150-plus missions,” Dmitra Ioannou, the deputy chief observer for the EU observation mission, was quoted as saying.

Pakistan is voting at a time when its foreign relations are the most damaged they have been in decades. Currently the US and Afghanistan accuse Islamabad of allowing Taliban militants and itscohorts, like the Haqqani group to operate out of sanctuaries in Pakistan. Also within the region meanwhile a standoff with archrival India over the disputed region of Kashmir grows ever more tense.

Just last month Pakistan was also placed back ona terror financing watch list. Pakistani officials attending a meeting in Paris had tried in vain to persuade the Financial Action Task Force (FATF) to keep Pakistan off a list of nations with inadequate controls to prevent terror financing and money laundering.

Pakistan was included on the watch list for three years until 2015, and FATF has now told the Islamabad government what needs to be done, in order for it to be taken off the list again.

For some time now Mr Khan despite hispast as an Oxford-educated, globetrotter has kept up a consistently anti-Americanism rhetoric in his political campaigning.

In doing so he has constantly thrown down the gauntlet to other Pakistani leaders for allowing the country to be used as a “ hired gun” by Washington.

Should the Pakistan military have been supporting his election campaign to the extent many believe then he will doubtless now have to tone down his criticism of Washington, leaving him kowtowing to the Pakistan army in foreign-policy matters.

The country’s military and intelligence establishment has long been the main beneficiary of security aid before its love affair with the US turned somewhat sour.

To that end now Pakistan’s generals are keen to salvage their relationship with the Washington and the Pentagon.

For the moment few expect the post election period to be anything other than an even more intensified struggle for control of the government. For decades now many analysts have warned that the military’s role in Pakistan’s volatile politics has only left the country in a permanent cycle of tumult and economic stagnation.

Whatever political manoeuvring now lies ahead among the country’s leaders, real power openly or otherwise will almost certainly stay in the hands of the Pakistan’s generals not any political party or Prime Minister. It seems for now the era of ‘hard coups’ has been replaced with a ‘silent coup’ period.