The loss was set up on the opening day itself, when electing to bat in overcast conditions India were reduced to 8 for 4 before being bowled out for 152 runs at Old Trafford.
"It is important to put runs on the board. The number 7, 8, 9, 10 and 11 batsmen have masked the top-order so far in this series," said Dhoni after trailing the five-match series 1-2.
"The win at Lord's also help camouflaged the poor form of the top-order and we couldn't question them that they are not scoring any runs. Our fifth bowler has scored more runs than our top-order batsmen.
"On this wicket, England bowled very well. The first hour of the match was very crucial. The batting department has to improve and the top five to six batsmen have to get more runs. This defeat will hurt us," he said
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The Indian batsmen didn't fare any better in the second innings as they were bowled out for 161 runs, this time in better conditions.
"We don't know what was going to happen tomorrow or day after. The important thing was to play out the day today," said Dhoni commenting on the weather forecast.
"Most of the batsmen have played cricket for a long time and have enough experience to know the match conditions. So they can see that they have to play out sessions accordingly. Sixty overs is a very big target, you can only plan ahead for 3-4 overs at the maximum. That is your target and that's the spell bowlers go through as well.