Protesters feel the trade deal will harm their economy and culture
Leading newspapers in Ecuador fear the current unrest could get out of hand and accuse the government of President Alfredo Palacios of failing to contain the crisis.
There is some sympathy for the concerns of the indigenous communities over a possible deal with the US which would lead to a free trade treaty, though many commentators feel it would benefit the country.
Some commentators put the blame on the nature of the political system, which they believe has failed to mature over the years to be able to tackle national issues in a rational manner.
There are also accusations that Venezuela's controversial President, Hugo Chavez, is influencing events.
Quito's La Hora is one of the papers which sympathises with the indigenous communities.
"The preoccupations of all sectors, especially the indigenous peoples and the peasants, is wholly understandable. If the trade negotiations fail to consider their situation, they will not be able to compete."
But, argues La Hora, "there appears to be little alternative but to sign up to the free trade agreement. Ecuador remains alone after our neighbours Colombia and Peru signed."
However, it calls for a fair treaty which takes into account the nation's needs. "Negotiating means giving and taking. Not capitulating. And the government needs to understand this in its talks with the US on a possible free trade accord."
An editorial in Hoy criticises indigenous leaders for organising the protests before the details of the accord have even been finalised.
"Their action is incoherent, especially as the negotiations have not even concluded and the details of how the key agricultural sector is to be opened have yet to be worked out."
"They have failed to present any alternative, instead causing huge damage to the economy with the blockades."
A leading daily in the main commercial city, Guayaquil, agrees with Hoy. El Universo condemns the protests as "irrational".
"The stoppages make no sense whatsoever to the ordinary citizen. Reject the free trade agreement? Okay, but negotiations are ongoing, nothing's been signed and the protesters don't tell us why we should oppose it nor what is the alternative."
El Universo also has tough words for the government. "We need a government which governs. The stability of presidents is vital. Ecuador doesn't need the demise of another president; but neither does it want an executive which fails to take action."
For another Guayaquil daily, Expreso, the rot set in long ago.
"In full view of every body, the country is falling apart, and lamentably, the government is not acting effectively to stop it."
Expreso argues that "this is a result of mistakes, corruption and diversions which happened long ago and have brought the country to the unbelievable state in which it currently finds itself".
It blames former governments as well as the current one for constantly seeking to put off problems by making pledges to social groups which are often not fulfilled, building up resentment which eventually explodes in social unrest.
El Comercio reports that the president is desperately seeking new allies to counter the bands of protesters.
Much of the comment canvassed from the general public by El Comercio is hostile to the protesters, especially their leaders.
"These indigenous groups are a minority manipulated by a few wearing golden ponchos, and don't have a clue what the free trade treaty is about," writes one correspondent. "We should explain it to these people who have been forgotten by the government since the oil boom."
"The peasants have been deceived," writes Gladys from Florida. She points the finger at "manipulators, probably from abroad. This smells like the work of [Venezuelan President Hugo] Chavez and the terrorists who help him. It's likely that his agents are manipulating the indigenous groups."
However, another correspondent, "Gatita", has more sympathy for the protesters. "It's not the best way to protest, but there's little else left to make the politicians stand up and take notice."
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